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Found 1 Document (0.653 seconds)

BMRB: 16372

2KKU

Solution structure of protein af2351 from Archaeoglobus fulgidus. Northeast Structural Genomics Consortium target AtT9/Ontario Center for Structural Proteomics Target af2351

Authors

Wu, B., Yee, A., Fares, C., Lemak, A., Rumpel, S., Semest, A., Arrowsmith, C.H.

Assembly

af2351

Entity

1. af2351 (polymer, Thiol state: all free), 139 monomers, 16659.43 Da Detail

MSKIVGVTYP IPKRFMDRFF KKGKDVFVKP ATVWKELKPG MKFVFYQSHE DTGFVGEARI KRVVLSENPM QFFETFGDRV FLTKDELKEY MKSQERWGRR RESKKKKLWM AIELEDVKKY DKPIKPKRLV PVGGQYLRE

Formula weight

16659.43 Da

Source organism

Archaeoglobus fulgidus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.2 %, Completeness: 86.9 %, Completeness (bb): 87.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.9 % (1566 of 1803)	88.7 % (853 of 962)	84.6 % (594 of 702)	85.6 % (119 of 139)
Backbone	87.8 % (718 of 818)	88.2 % (246 of 279)	88.2 % (360 of 408)	85.5 % (112 of 131)
Sidechain	86.7 % (967 of 1115)	88.9 % (607 of 683)	83.3 % (353 of 424)	87.5 % (7 of 8)
Aromatic	68.4 % (130 of 190)	85.3 % (81 of 95)	50.0 % (46 of 92)	100.0 % (3 of 3)
Methyl	98.3 % (118 of 120)	98.3 % (59 of 60)	98.3 % (59 of 60)

1. af2351

MSKIVGVTYP IPKRFMDRFF KKGKDVFVKP ATVWKELKPG MKFVFYQSHE DTGFVGEARI KRVVLSENPM QFFETFGDRV FLTKDELKEY MKSQERWGRR RESKKKKLWM AIELEDVKKY DKPIKPKRLV PVGGQYLRE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
9	bis-tris	natural abundance	25 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.01 %
12	benzamidine	natural abundance	1 mM
13	D2O	natural abundance	99.9 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
14	af2351	[U-7% 13C; U-99% 15N]	0.5 mM
15	bis-tris	natural abundance	25 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.01 %
18	benzamidine	natural abundance	1 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.01 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.01 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: 0.05 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.76 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-06-29

Citation

Solution structure of protein af2351 from Archaeoglobus fulgidus. Northeast Structural Genomics Consortium target AtT9/Ontario Center for Structural Proteomics Target af2351
Wu, B., Yee, A., Fares, C., Lemak, A., Rumpel, S., Semest, A., Arrowsmith, C.H.
Not known

Related entities 1. af2351, : 1 : 2 entities Detail

Experiments performed 11 experiments Detail

1 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

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 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

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 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

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 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

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 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

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
2	bis-tris	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 99.9% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	af2351	[U-100% 13C; U-100% 15N]	0.5 mM
9	bis-tris	natural abundance	25 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.01 %
12	benzamidine	natural abundance	1 mM
13	D2O	natural abundance	99.9 %

11 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

#	Name	Isotope labeling	Concentration
14	af2351	[U-7% 13C; U-99% 15N]	0.5 mM
15	bis-tris	natural abundance	25 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.01 %
18	benzamidine	natural abundance	1 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16372_2kku.nef
Input source #2: Coordindates	2kku.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--------
MGSSHHHHHHSSGRENLYFQGHMSKIVGVTYPIPKRFMDRFFKKGKDVFVKPATVWKELKPGMKFVFYQSHEDTGFVGEARIKRVVLSENPMQFFETFGD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGHMSKIVGVTYPIPKRFMDRFFKKGKDVFVKPATVWKELKPGMKFVFYQSHEDTGFVGEARIKRVVLSENPMQFFETFGD
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

80--------90-------100-------110-------120-------130---------
RVFLTKDELKEYMKSQERWGRRRESKKKKLWMAIELEDVKKYDKPIKPKRLVPVGGQYLRE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RVFLTKDELKEYMKSQERWGRRRESKKKKLWMAIELEDVKKYDKPIKPKRLVPVGGQYLRE
-------110-------120-------130-------140-------150-------160-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	161	0	0	100.0

Content subtype: combined_16372_2kku.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1525		80.1 (chain: A, length: 161)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4348 (1)	noe	78.9 (chain: A, length: 161)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	141 (1)	hbond	33.5 (chain: A, length: 161)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	162 (162)	.	70.8 (chain: A, length: 161)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 161, Sequence coverage: 80.1%
- Total number of assignments
  - ¹H chemical shifts: 837
  - ¹³C chemical shifts: 574
  - ¹⁵N chemical shifts: 114
- 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)
83	THR	HG1	5.482

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1089	836	76.8
¹³C chemical shifts	797	574	72.0
¹⁵N chemical shifts	175	114	65.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	326	240	73.6
¹³C chemical shifts	322	231	71.7
¹⁵N chemical shifts	153	107	69.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	763	596	78.1
¹³C chemical shifts	475	343	72.2
¹⁵N chemical shifts	22	7	31.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	63	91.3
¹³C chemical shifts	69	62	89.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	81	68.6
¹³C chemical shifts	115	44	38.3
¹⁵N chemical shifts	3	3	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: 161, Sequence coverage: 78.9%
- Total number of restraints: 4348
- Weight of restraints: 1.0 (4348)
- Potential type of restraints: square-well-parabolic (4348)
- Range of distance target values: 2.25, 3.9 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 161, Sequence coverage: 33.5%
  - Total number of restraints: 141
  - Weight of restraints: 1.0 (141)
  - Potential type of restraints: square-well-parabolic (141)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 161, Sequence coverage: 70.8%
- Total number of restraints: 162
- Total number of restraints per polymer type: 162
- Weight of restraints: 1.0 (162)
- Potential type of restraints: square-well-parabolic (162)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords alpha/beta protein

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Found 1 Document (0.653 seconds)

BMRB: 16372

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. af2351, : 1 : 2 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail