BMRBj - BMREntryMaster

Found 1 Document (0.662 seconds)

BMRB: 16774

2KVC

Solution structure of the Mycobacterium tuberculosis protein Rv0543c, a member of the DUF3349 superfamily. Seattle Structural Genomics Center for Infectious Disease (SSGCID) target MytuD.17112.a

Authors

Buchko, G.W., Kim, C.Y., Thomas, T.C.

Assembly

Rv0543c

Entity

1. Rv0543c (polymer, Thiol state: all free), 103 monomers, 11592.95 Da Detail

GSHMNRFLTS IVAWLRAGYP EGIPPTDSFA VLALLCRRLS HDEVKAVANE LMRLGDFDQI DIGVVITHFT DELPSPEDVE RVRARLAAQG WPLDDVRDRE EHA

Formula weight

11592.95 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.6 %, Completeness (bb): 92.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.6 % (1073 of 1172)	91.9 % (556 of 605)	90.9 % (422 of 464)	92.2 % (95 of 103)
Backbone	92.4 % (560 of 606)	94.2 % (194 of 206)	91.4 % (277 of 303)	91.8 % (89 of 97)
Sidechain	91.7 % (608 of 663)	90.7 % (362 of 399)	93.0 % (240 of 258)	100.0 % (6 of 6)
Aromatic	84.1 % (74 of 88)	84.1 % (37 of 44)	83.3 % (35 of 42)	100.0 % (2 of 2)
Methyl	93.8 % (120 of 128)	93.8 % (60 of 64)	93.8 % (60 of 64)

1. Rv0543c

GSHMNRFLTS IVAWLRAGYP EGIPPTDSFA VLALLCRRLS HDEVKAVANE LMRLGDFDQI DIGVVITHFT DELPSPEDVE RVRARLAAQG WPLDDVRDRE EHA

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
5	Rv0543c	natural abundance	1-2 (±0.2) mM
6	sodium chloride	natural abundance	300 (±10.0) mM
7	TRIS	natural abundance	20 (±2.0) mM
8	DTT	natural abundance	1 (±0.2) mM

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: -0.1 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: -0.1 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: 0.0 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: -0.11 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2KVC, Strand ID: A Detail

Release date

2010-03-21

Citation

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c
Buchko, G.W., Phan, I., Myler, P.J., Terwilliger, T.C., Kim, C.
Arch. Biochem. Biophys. (2011), 506, 150-156, PubMed 21144816 , DOI 10.1016/j.abb.2010.12.001 , Abstract

Related entities 1. Rv0543c, : 1 : 1 : 6 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

2 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

3 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

4 3D HN(COCA)CB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

5 3D HNCO

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

6 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

9 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
5	Rv0543c	natural abundance	1-2 (±0.2) mM
6	sodium chloride	natural abundance	300 (±10.0) mM
7	TRIS	natural abundance	20 (±2.0) mM
8	DTT	natural abundance	1 (±0.2) mM

10 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	Rv0543c	natural abundance	1-2 (±0.2) mM
2	sodium chloride	natural abundance	300 (±10.0) mM
3	TRIS	natural abundance	20 (±2.0) mM
4	DTT	natural abundance	1 (±0.2) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16774_2kvc.nef
Input source #2: Coordindates	2kvc.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
GSHMNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDRE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMNRFLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDVERVRARLAAQGWPLDDVRDRE

---
EHA
|||
EHA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	103	0	0	100.0

Content subtype: combined_16774_2kvc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1059		99.0 (chain: A, length: 103)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1433 (1)	noe	95.1 (chain: A, length: 103)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	64 (1)	hbond	46.6 (chain: A, length: 103)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	132 (132)	.	79.6 (chain: A, length: 103)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 547
  - ¹³C chemical shifts: 418
  - ¹⁵N chemical shifts: 94
- 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	605	546	90.2
¹³C chemical shifts	464	418	90.1
¹⁵N chemical shifts	113	94	83.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	206	189	91.7
¹³C chemical shifts	206	178	86.4
¹⁵N chemical shifts	97	88	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	399	357	89.5
¹³C chemical shifts	258	240	93.0
¹⁵N chemical shifts	16	6	37.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	62	93.9
¹³C chemical shifts	66	62	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	36	81.8
¹³C chemical shifts	42	35	83.3
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 95.1%
- Total number of restraints: 1429
- Weight of restraints: 1.0 (1429)
- Potential type of restraints: square-well-parabolic (1429)
- Range of distance target values: 2.33, 3.67 (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_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 46.6%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Range of distance target values: 1.1, 1.85 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 79.6%
- Total number of restraints: 132
- Total number of restraints per polymer type: 132
- Weight of restraints: 1.0 (132)
- Potential type of restraints: square-well-parabolic (132)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, SSGCID, tuberculosis

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Found 1 Document (0.662 seconds)

BMRB: 16774

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Rv0543c, : 1 : 1 : 6 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail