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Found 1 Document (0.746 seconds)

BMRB: 16517

2KOK

Solution structure of an arsenate reductase (ArsC) related protein from Brucella melitensis. Seattle Structural Genomics Center for Infectious Disease (SSGCID) target BrabA.00007.a.

Authors

Buchko, G.W.

Assembly

BR7

Entity

1. BR7 (polymer, Thiol state: all free), 120 monomers, 13756.69 Da Detail

GPGSMSVTIY GIKNCDTMKK ARIWLEDHGI DYTFHDYKKE GLDAETLDRF LKTVPWEQLL NRAGTTFRKL PEDVRSNVDA ASARELMLAQ PSMVKRPVLE RDGKLMVGFK PAQYEAYFKL

Formula weight

13756.69 Da

Source organism

Brucella melitensis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 91.3 %, Completeness (bb): 95.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (1311 of 1436)	88.4 % (665 of 752)	94.0 % (528 of 562)	96.7 % (118 of 122)
Backbone	95.3 % (675 of 708)	94.2 % (228 of 242)	95.5 % (336 of 352)	97.4 % (111 of 114)
Sidechain	89.0 % (748 of 840)	85.7 % (437 of 510)	94.4 % (304 of 322)	87.5 % (7 of 8)
Aromatic	90.2 % (110 of 122)	90.2 % (55 of 61)	89.8 % (53 of 59)	100.0 % (2 of 2)
Methyl	93.5 % (116 of 124)	93.5 % (58 of 62)	93.5 % (58 of 62)

1. BR7

GPGSMSVTIY GIKNCDTMKK ARIWLEDHGI DYTFHDYKKE GLDAETLDRF LKTVPWEQLL NRAGTTFRKL PEDVRSNVDA ASARELMLAQ PSMVKRPVLE RDGKLMVGFK PAQYEAYFKL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
7	BR7	natural abundance	1.0 (±0.2) mM
8	sodium chloride	natural abundance	100 (±3.0) mM
9	TRIS	natural abundance	20 (±1.0) mM
10	DTT	natural abundance	1 (±0.2) mM
11	D2O	natural abundance	100 %

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: -0.35 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: -0.35 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: -0.05 ppm, Outliers: 2 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: 0.18 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-10-22

Citation

Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis
Buchko, G.W., Hewitt, S.N., Napuli, A.J., Van Voorhis, W.C., Myler, P.J.
Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. (2011), 67, 1129-1136, PubMed 21904062 , DOI 10.1107/S1744309111006336 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25195 released on 2014-09-14
Title Solution structure of a putative arsenate reductase from Brucella melitensis. Seattle Structural Genomics Center for Infectious Disease target BrabA.00073.a

Related entities 1. BR7, : 1 : 46 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 3D HN(CO)CA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D C(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 3D H(CCO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 deuterium exchange

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
7	BR7	natural abundance	1.0 (±0.2) mM
8	sodium chloride	natural abundance	100 (±3.0) mM
9	TRIS	natural abundance	20 (±1.0) mM
10	DTT	natural abundance	1 (±0.2) mM
11	D2O	natural abundance	100 %

11 3D HBHA_CO_NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 (±0.5) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Concentration
1	BR7	natural abundance	1.5 (±0.2) mM
2	sodium chloride	natural abundance	100 (±3.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.2) mM
5	H2O	natural abundance	90 %
6	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_16517_2kok.nef
Input source #2: Coordindates	2kok.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
GPGSMSVTIYGIKNCDTMKKARIWLEDHGIDYTFHDYKKEGLDAETLDRFLKTVPWEQLLNRAGTTFRKLPEDVRSNVDAASARELMLAQPSMVKRPVLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSMSVTIYGIKNCDTMKKARIWLEDHGIDYTFHDYKKEGLDAETLDRFLKTVPWEQLLNRAGTTFRKLPEDVRSNVDAASARELMLAQPSMVKRPVLE

-------110-------120
RDGKLMVGFKPAQYEAYFKL
||||||||||||||||||||
RDGKLMVGFKPAQYEAYFKL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	120	0	0	100.0

Content subtype: combined_16517_2kok.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1289		99.2 (chain: A, length: 120)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	1979 (1)	noe	95.8 (chain: A, length: 120)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	168 (1)	hbond	54.2 (chain: A, length: 120)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	188 (188)	.	97.5 (chain: A, length: 120)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 652
  - ¹³C chemical shifts: 519
  - ¹⁵N chemical shifts: 118
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	752	652	86.7
¹³C chemical shifts	562	519	92.3
¹⁵N chemical shifts	130	118	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	242	227	93.8
¹³C chemical shifts	240	220	91.7
¹⁵N chemical shifts	114	111	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	510	425	83.3
¹³C chemical shifts	322	299	92.9
¹⁵N chemical shifts	16	7	43.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	60	89.6
¹³C chemical shifts	67	60	89.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	55	90.2
¹³C chemical shifts	59	53	89.8
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 95.8%
- Total number of restraints: 1979
- Weight of restraints: 1.0 (1979)
- Potential type of restraints: upper-bound-parabolic (1979)
- Range of distance target values: 2.35, 5.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 54.2%
  - Total number of restraints: 168
  - Weight of restraints: 1.0 (168)
  - Potential type of restraints: upper-bound-parabolic (168)
  - Range of distance target values: 1.8, 3.0 (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: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 97.5%
- Total number of restraints: 188
- Total number of restraints per polymer type: 188
- Weight of restraints: 1.0 (188)
- Potential type of restraints: square-well-parabolic (188)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords arsenate reductase, brucellosis, SSGCID, zoonotic

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Found 1 Document (0.746 seconds)

BMRB: 16517

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. BR7, : 1 : 46 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail