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Found 1 Document (0.688 seconds)

BMRB: 15849

2K5V

SOLUTION NMR STRUCTURE OF the second OB-fold domain of replication protein A from Methanococcus maripaludis. NORTHEAST STRUCTURAL GENOMICS TARGET MrR110B.

Authors

Aramini, J.M., Maglaqui, M., Jiang, M., Ciccosanti, C., Xiao, R., Nair, R., Everett, J.K., Swapna, G.V.T., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

MrR110B

Entity

1. MrR110B (polymer, Thiol state: not present), 104 monomers, 11611.96 Da Detail

MNYKISELMP NLSGTINAEV VAAYPKKEFS RKDGTKGQLK SLFLKDDTGS IRGTLWNELA DFEVKKGDIA EVSGYVKQGY SGLEISVDNI GIIEKSLEHH HHHH

Formula weight

11611.96 Da

Source organism

Methanococcus maripaludis

Exptl. method

solution NMR

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.2 %, Completeness: 92.8 %, Completeness (bb): 93.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.8 % (1127 of 1214)	92.7 % (585 of 631)	92.6 % (438 of 473)	94.5 % (104 of 110)
Backbone	93.4 % (579 of 620)	93.5 % (202 of 216)	93.0 % (281 of 302)	94.1 % (96 of 102)
Sidechain	92.3 % (635 of 688)	92.3 % (383 of 415)	92.1 % (244 of 265)	100.0 % (8 of 8)
Aromatic	75.5 % (74 of 98)	75.5 % (37 of 49)	75.0 % (36 of 48)	100.0 % (1 of 1)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. MrR110B

MNYKISELMP NLSGTINAEV VAAYPKKEFS RKDGTKGQLK SLFLKDDTGS IRGTLWNELA DFEVKKGDIA EVSGYVKQGY SGLEISVDNI GIIEKSLEHH HHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	calcium chloride	natural abundance	5 mM
11	DTT	natural abundance	10 mM
12	sodium azide	natural abundance	0.02 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	MrR110B	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	calcium chloride	natural abundance	5 mM
17	DTT	natural abundance	10 mM
18	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: -0.08 ppm, Outliers: 3 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: -0.08 ppm, Outliers: 3 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: -0.18 ppm, Outliers: 3 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: 0.71 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K5V, Strand ID: A Detail

Release date

2008-06-30

Citation

SOLUTION NMR STRUCTURE OF the second OB-fold domain of replication protein A from Methanococcus maripaludis. NORTHEAST STRUCTURAL GENOMICS TARGET MrR110B
Aramini, J.M., Maglaqui, M., Jiang, M., Ciccosanti, C., Xiao, R., Nair, R., Everett, J.K., Swapna, G.V.T., Acton, T.B., Montelione, G.T.
Not known

Related entities 1. MrR110B, : 1 : 1 : 6 entities Detail

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

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

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

4 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

8 3D HCCH-COSY aliphatic

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

9 3D HCCH-TOCSY aliphatic

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

10 3D CCH-TOCSY aliphatic

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

11 3D HNHA

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

12 3D simultaneous CN NOESY

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

14 3D simultaneous CN NOESY

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
8	MES	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	calcium chloride	natural abundance	5 mM
11	DTT	natural abundance	10 mM
12	sodium azide	natural abundance	0.02 %

15 2D 1H-13C HSQC high res. (L/V stereoassignment)

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	MrR110B	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	calcium chloride	natural abundance	5 mM
17	DTT	natural abundance	10 mM
18	sodium azide	natural abundance	0.02 %

16 2D 1H-15N hetNOE

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	MrR110B	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	calcium chloride	natural abundance	5 mM
17	DTT	natural abundance	10 mM
18	sodium azide	natural abundance	0.02 %

17 2D 1H-15N T1

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	MrR110B	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	calcium chloride	natural abundance	5 mM
17	DTT	natural abundance	10 mM
18	sodium azide	natural abundance	0.02 %

18 2D 1H-13C HSQC (arom)

Instrument

Bruker Avance - 800 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MrR110B	[U-100% 13C; U-100% 15N]	1.18 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %

19 2D 1H-15N T2

Instrument

Bruker Avance - 600 MHz 5mm CRP

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	MrR110B	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium chloride	natural abundance	100 mM
16	calcium chloride	natural abundance	5 mM
17	DTT	natural abundance	10 mM
18	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_15849_2k5v.nef
Input source #2: Coordindates	2k5v.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

------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-
MNYKISELMPNLSGTINAEVVAAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELADFEVKKGDIAEVSGYVKQGYSGLEISVDNIGIIEKSLEHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNYKISELMPNLSGTINAEVVAAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELADFEVKKGDIAEVSGYVKQGYSGLEISVDNIGIIEKSLEHH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----
HHHH
||||
HHHH
----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	0	100.0

Content subtype: combined_15849_2k5v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1149		94.2 (chain: A, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2314 (1)	noe	94.2 (chain: A, length: 104)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	125 (125)	.	80.8 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 94.2%
- Total number of assignments
  - ¹H chemical shifts: 594
  - ¹³C chemical shifts: 450
  - ¹⁵N chemical shifts: 105
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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)
173	ASN	CG	176.802
182	ASN	CG	178.798
188	ASN	CG	176.69
209	GLN	CD	180.064
228	ASN	CG	176.924
249	GLN	CD	179.673
260	ASN	CG	176.738

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	631	594	94.1
¹³C chemical shifts	473	443	93.7
¹⁵N chemical shifts	112	105	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	216	203	94.0
¹³C chemical shifts	208	196	94.2
¹⁵N chemical shifts	102	95	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	415	391	94.2
¹³C chemical shifts	265	247	93.2
¹⁵N chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	57	100.0
¹³C chemical shifts	57	57	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	37	75.5
¹³C chemical shifts	48	36	75.0
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: 104, Sequence coverage: 94.2%
- Total number of restraints: 2310
- Weight of restraints: 1.0 (2310)
- Potential type of restraints: square-well-parabolic (2310)
- Range of distance target values: 2.17, 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: 104, Sequence coverage: 80.8%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords OB-fold domain, replication protein A, solution NMR structure

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Found 1 Document (0.688 seconds)

BMRB: 15849

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MrR110B, : 1 : 1 : 6 entities Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 4 contents Detail