BMRBj - BMREntryMaster

Found 1 Document (0.957 seconds)

BMRB: 30421

6CKQ

Solution structure of the Burkholderia thailandensis transcription antitermination protein NusB (BTH_I1529) - Seattle Structural Genomics Center for Infectious Disease target ButhA.17903.a

Authors

Buchko, G.W., Seattle Structural Genomics Center for Infectious Disease, S.

Assembly

Transcription antitermination protein NusB

Entity

1. Transcription antitermination protein NusB (polymer, Thiol state: not present), 149 monomers, 16279.36 Da Detail

GPGSMKKSAR RQSRELATQG LYQWLLSNAA PGEIDAQLRG ALGYDKADKT LLDTILHGVI REHATLAEAI SPSLDRPIDQ LSPVERAVLL IATYELTHQI ETPYRVIINE AVELAKTFGG SDGYKYVNGV LDKLAVKLRP AETQARRGA

Formula weight

16279.36 Da

Source organism

Burkholderia thailandensis E264

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 81.8 %, Completeness (bb): 88.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.8 % (1387 of 1696)	77.5 % (682 of 880)	84.2 % (558 of 663)	96.1 % (147 of 153)
Backbone	88.1 % (775 of 880)	88.1 % (267 of 303)	85.3 % (371 of 435)	96.5 % (137 of 142)
Sidechain	78.5 % (748 of 953)	71.9 % (415 of 577)	88.5 % (323 of 365)	90.9 % (10 of 11)
Aromatic	84.1 % (69 of 82)	82.9 % (34 of 41)	85.0 % (34 of 40)	100.0 % (1 of 1)
Methyl	88.4 % (175 of 198)	84.8 % (84 of 99)	91.9 % (91 of 99)

1. entity 1

GPGSMKKSAR RQSRELATQG LYQWLLSNAA PGEIDAQLRG ALGYDKADKT LLDTILHGVI REHATLAEAI SPSLDRPIDQ LSPVERAVLL IATYELTHQI ETPYRVIINE AVELAKTFGG SDGYKYVNGV LDKLAVKLRP AETQARRGA

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.4) K, pH 7 (±0.1), Details 1 mM [U-99% 13C; U-99% 15N] NusB, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

LACS Plot; CA

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

Referencing offset: -0.36 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.36 ppm, Outliers: 1 Detail

LACS Plot; HA

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

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	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.17 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6CKQ, Strand ID: A Detail

Release date

2018-03-26

Citation

Solution structure of the Burkholderia thailandensis transcription antitermination protein NusB (BTH_I1529)
Buchko, G.W., SSGCID, S.

Related entities 1. Transcription antitermination protein NusB, : 1 : 1 : 116 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent VXRS - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.4) K, pH 7 (±0.1), Details 1 mM [U-99% 13C; U-99% 15N] NusB, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

4 3D HNCO

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

5 3D HNCACB

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

6 2D Deltas

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

7 deuterium exchange

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

8 3D 1H-13C NOESY aromatic

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

9 3D 1H-13C NOESY aliphatic

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

10 3D 1H-15N NOESY

Instrument

Agilent VXRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

11 3D C(CO)NH

Instrument

Varian VXRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NusB	[U-99% 13C; U-99% 15N]	1 (±0.3) mM
2	sodium chloride	natural abundance	100 (±0.05) mM
3	TRIS	natural abundance	20 (±0.05) mM
4	DTT	natural abundance	1 (±0.02) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30421_6ckq.nef
Input source #2: Coordindates	6ckq.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
GPGSMKKSARRQSRELATQGLYQWLLSNAAPGEIDAQLRGALGYDKADKTLLDTILHGVIREHATLAEAISPSLDRPIDQLSPVERAVLLIATYELTHQI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSMKKSARRQSRELATQGLYQWLLSNAAPGEIDAQLRGALGYDKADKTLLDTILHGVIREHATLAEAISPSLDRPIDQLSPVERAVLLIATYELTHQI

-------110-------120-------130-------140---------
ETPYRVIINEAVELAKTFGGSDGYKYVNGVLDKLAVKLRPAETQARRGA
|||||||||||||||||||||||||||||||||||||||||||||||||
ETPYRVIINEAVELAKTFGGSDGYKYVNGVLDKLAVKLRPAETQARRGA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	149	0	0	100.0

Content subtype: combined_30421_6ckq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1351		99.3 (chain: A, length: 149)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	1849 (1)	noe	94.0 (chain: A, length: 149)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	72 (1)	hbond	39.6 (chain: A, length: 149)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	232 (232)	.	91.9 (chain: A, length: 149)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 99.3%
- Total number of assignments
  - ¹³C chemical shifts: 543
  - ¹H chemical shifts: 661
  - ¹⁵N chemical shifts: 147
- 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)
143	THR	HG1	4.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	663	543	81.9
¹H chemical shifts	880	660	75.0
¹⁵N chemical shifts	164	147	89.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	298	227	76.2
¹H chemical shifts	303	264	87.1
¹⁵N chemical shifts	142	137	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	365	316	86.6
¹H chemical shifts	577	396	68.6
¹⁵N chemical shifts	22	10	45.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	100	89	89.0
¹H chemical shifts	100	82	82.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	40	34	85.0
¹H chemical shifts	41	35	85.4
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 94.0%
- Total number of restraints: 1849
- Weight of restraints: 1.0 (1849)
- Potential type of restraints: square-well-parabolic (1849)
- Range of distance target values: 2.04, 3.65 (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: 149, Sequence coverage: 39.6%
  - Total number of restraints: 72
  - Weight of restraints: 1.0 (72)
  - Potential type of restraints: square-well-parabolic (72)
  - Range of distance target values: 1.25, 2.85 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 91.9%
- Total number of restraints: 232
- Total number of restraints per polymer type: 232
- Weight of restraints: 1.0 (232)
- Potential type of restraints: square-well-parabolic (232)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NusA, SSGCID, Seattle Structural Genomics Center for Infectious Disease, Structural Genomics, TRANSCRIPTION, infectious disease model, transcription antitermnation

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Found 1 Document (0.957 seconds)

BMRB: 30421

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Transcription antitermination protein NusB, : 1 : 1 : 116 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail