BMRBj - BMREntryMaster

Found 1 Document (0.706 seconds)

BMRB: 15819

2K50

Solution NMR Structure of the replication Factor A Related Protein from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Target TR91A.

Authors

Rossi, P., Xiao, R., Maglaqui, M., Foote, E.L., Ciccosanti, C., Swapna, G., Acton, T.B., Rost, B., Everett, J.K., Montelione, G.T.

Assembly

TR91A

Entity

1. TR91A (polymer, Thiol state: not present), 110 monomers, 12455.26 Da Detail

MKPEHRMDTI SKLEEGAETP VTGRVMKISS PRTFTTRKGR EGKLANVIIA DDTGELRAVF WTENIKLLKK FREGDVIRIK DVNIRGGFGG RKEAHLMPRS TVEVLDPLEH

Formula weight

12455.26 Da

Source organism

Methanothermobacter thermautotrophicus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 91.9 %, Completeness (bb): 94.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.9 % (1192 of 1297)	89.5 % (611 of 683)	94.7 % (478 of 505)	94.5 % (103 of 109)
Backbone	94.6 % (615 of 650)	92.9 % (209 of 225)	96.2 % (308 of 320)	93.3 % (98 of 105)
Sidechain	89.3 % (667 of 747)	86.9 % (398 of 458)	93.0 % (265 of 285)	100.0 % (4 of 4)
Aromatic	87.5 % (56 of 64)	87.5 % (28 of 32)	87.1 % (27 of 31)	100.0 % (1 of 1)
Methyl	96.8 % (120 of 124)	95.2 % (59 of 62)	98.4 % (61 of 62)

1. TR91A

MKPEHRMDTI SKLEEGAETP VTGRVMKISS PRTFTTRKGR EGKLANVIIA DDTGELRAVF WTENIKLLKK FREGDVIRIK DVNIRGGFGG RKEAHLMPRS TVEVLDPLEH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.008

#	Name	Isotope labeling	Concentration
7	TR91A	[U-100% 15N; 5% 13C]	1.33 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	100 mM
11	Calcium Chloride	natural abundance	5 mM
12	sodium azide	natural abundance	0.02 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.26 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K50, Strand ID: A Detail

Release date

2008-08-07

Citation

Solution NMR Structure of the replication Factor A Related Protein from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Target TR91A
Rossi, P., Xiao, R., Acton, T.B., Montelione, G.T.
Not known

Related entities 1. TR91A, : 1 : 12 entities Detail

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.008

#	Name	Isotope labeling	Concentration
7	TR91A	[U-100% 15N; 5% 13C]	1.33 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	100 mM
11	Calcium Chloride	natural abundance	5 mM
12	sodium azide	natural abundance	0.02 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

3 2D 1H-13C HSQC (arom)

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

6 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

10 3D CCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

11 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

12 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

13 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

14 3D 1H-13C NOESY (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

15 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.008

#	Name	Isotope labeling	Concentration
7	TR91A	[U-100% 15N; 5% 13C]	1.33 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	100 mM
11	Calcium Chloride	natural abundance	5 mM
12	sodium azide	natural abundance	0.02 %

16 2D HET NOE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.008

#	Name	Isotope labeling	Concentration
7	TR91A	[U-100% 15N; 5% 13C]	1.33 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	100 mM
11	Calcium Chloride	natural abundance	5 mM
12	sodium azide	natural abundance	0.02 %

17 Pseudo 2D T1

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.008

#	Name	Isotope labeling	Concentration
7	TR91A	[U-100% 15N; 5% 13C]	1.33 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	100 mM
11	Calcium Chloride	natural abundance	5 mM
12	sodium azide	natural abundance	0.02 %

18 Pseudo 2D T2 (CPMG)

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.008

#	Name	Isotope labeling	Concentration
7	TR91A	[U-100% 15N; 5% 13C]	1.33 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	100 mM
11	Calcium Chloride	natural abundance	5 mM
12	sodium azide	natural abundance	0.02 %

19 3D 1H-13C NOESY (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

20 2D 1H-13C HSQC (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

21 2D 1H-13C HSQC (stereomethyl)

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NESG PST ID: TR91A.006

#	Name	Isotope labeling	Concentration
1	TR91A	[U-100% 13C; U-100% 15N]	1.25 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	100 mM
5	Calcium Chloride	natural abundance	5 mM
6	sodium azide	natural abundance	0.02 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15819_2k50.nef
Input source #2: Coordindates	2k50.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MKPEHRMDTISKLEEGAETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIKLLKKFREGDVIRIKDVNIRGGFGGRKEAHLMPRS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKPEHRMDTISKLEEGAETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIKLLKKFREGDVIRIKDVNIRGGFGGRKEAHLMPRS

-------110-----
TVEVLDPLEHHHHHH
|||||||||||||||
TVEVLDPLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_15819_2k50.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1209		93.0 (chain: A, length: 115)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2310 (1)	noe	92.2 (chain: A, length: 115)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	214 (214)	.	77.4 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 93.0%
- Total number of assignments
  - ¹H chemical shifts: 631
  - ¹³C chemical shifts: 475
  - ¹⁵N chemical shifts: 103
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
95	HIS	ND1	250.13
95	HIS	NE2	169.327
100	SER	HG	6.129

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	713	630	88.4
¹³C chemical shifts	530	475	89.6
¹⁵N chemical shifts	125	101	80.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	235	213	90.6
¹³C chemical shifts	230	208	90.4
¹⁵N chemical shifts	110	97	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	478	417	87.2
¹³C chemical shifts	300	267	89.0
¹⁵N chemical shifts	15	4	26.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	65	98.5
¹³C chemical shifts	66	65	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	28	66.7
¹³C chemical shifts	41	27	65.9
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 92.2%
- Total number of restraints: 2310
- Weight of restraints: 1.0 (2310)
- Potential type of restraints: square-well-parabolic (2310)
- Range of distance target values: 2.29, 3.92 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 77.4%
- Total number of restraints: 214
- Total number of restraints per polymer type: 214
- Weight of restraints: 1.0 (214)
- Potential type of restraints: square-well-parabolic (214)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.706 seconds)

BMRB: 15819

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. TR91A, : 1 : 12 entities Detail

Experiments performed 21 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail