BMRB Entry 16846

Name: Central B domain of Rv0899 from Mycobacterium tuberculosis
Published: 2010-05-10

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PDB ID: 2ksm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16846
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Central B domain of Rv0899 from Mycobacterium tuberculosis

Deposition date:

2010-04-07

Original release date:

2010-05-10

Authors:

Teriete, Peter; Yao, Yong; Kolodzik, Adrian; Niederweis, Michael; Marassi, Francesca

Citation:

Citation: Teriete, Peter; Yao, Yong; Kolodzik, Adrian; Yu, Jinghua; Song, Houhui; Niederweis, Michael; Marassi, Francesca. "Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel" Biochemistry 49, 2768-2777 (2010).
PubMed: 20199110

Assembly members:

Assembly members:
Rv0899, polymer, 131 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Mycobacterium tuberculosis Taxonomy ID: 1773 Superkingdom: Bacteria Kingdom: not available Genus/species: Mycobacterium tuberculosis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rv0899: GASALSLSLLSISRSGNTVT LIGDFPDEAAKAALMTALNG LLAPGVNVIDQIHVDPVVRS LDFSSAEPVFTASVPIPDFG LKVERDTVTLTGTAPSSEHK DAVKRAATSTWPDMKIVNNI EVTGQAPPGPP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	536
15N chemical shifts	126
1H chemical shifts	818

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Rv0899	1

Entities:

Entity 1, Rv0899 131 residues - Formula weight is not available

residues 73 to 203

1

GLY

ALA

SER

ALA

LEU

SER

LEU

SER

LEU

2

SER

ILE

SER

ARG

SER

GLY

ASN

THR

VAL

THR

3

LEU

ILE

GLY

ASP

PHE

PRO

ASP

GLU

ALA

4

LYS

ALA

LEU

MET

THR

ALA

LEU

ASN

GLY

5

LEU

ALA

PRO

GLY

VAL

ASN

VAL

ILE

ASP

6

GLN

ILE

HIS

VAL

ASP

PRO

VAL

ARG

SER

7

LEU

ASP

PHE

SER

ALA

GLU

PRO

VAL

PHE

8

THR

ALA

SER

VAL

PRO

ILE

PRO

ASP

PHE

GLY

9

LEU

LYS

VAL

GLU

ARG

ASP

THR

VAL

THR

LEU

10

THR

GLY

THR

ALA

PRO

SER

GLU

HIS

LYS

11

ASP

ALA

VAL

LYS

ARG

ALA

THR

SER

THR

12

TRP

PRO

ASP

MET

LYS

ILE

VAL

ASN

ILE

13

GLU

VAL

THR

GLY

GLN

ALA

PRO

GLY

PRO

14

PRO

Samples:

NMR_sample: Rv0899(73-220), [U-99% 15N], 1.7 ± 0.1 mM; Rv0899(73-220), [U-99% 13C; U-99% 15N], 1 ± 0.1 mM; phosphate 5 mM; H2O 95%; D2O 5%

D2O_sample: Rv0899(73-220), [U-99% 13C; U-99% 15N], 1 ± 0.1 mM; Rv0899(73-220), [U-99% 15N], 0.3 ± 0.1 mM; D2O 100%; phosphate 5 mM

RDC_Pf1: Rv0899(73-220), [U-99% 15N], 0.4 ± 0.1 mM; Pf1 phage 15 mg/ml; phosphate 5 mM; H2O 95%; D2O 5%

RDC_fd: Rv0899(73-220), [U-99% 15N], 0.4 ± 0.1 mM; fd phage 10 mg/ml; phosphate 5 mM; H2O 95%; D2O 5%; KCl 200 mM

RDC_stressed_gel: Rv0899 73-220, [U-99% 15N], 0.4 ± 0.1 mM; polyacrylamide gel 4.5%; phosphate 5 mM; H2O 95%; D2O 5%

sample_conditions: ionic strength: 0.005 M; pH: 7; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NMR_sample	isotropic	sample_conditions
IPAP	RDC_Pf1	anisotropic	sample_conditions
IPAP	RDC_fd	anisotropic	sample_conditions
IPAP	RDC_stressed_gel	anisotropic	sample_conditions
2D 1H-13C HSQC	NMR_sample	isotropic	sample_conditions
3D HNCA	NMR_sample	isotropic	sample_conditions
3D HNCACB	NMR_sample	isotropic	sample_conditions
3D C(CO)NH	NMR_sample	isotropic	sample_conditions
3D HCCH-TOCSY	D2O_sample	isotropic	sample_conditions
3D 1H-15N NOESY	NMR_sample	isotropic	sample_conditions
3D 1H-15N TOCSY	NMR_sample	isotropic	sample_conditions
3D 1H-13C NOESY	NMR_sample	isotropic	sample_conditions
3D HNCO	NMR_sample	isotropic	sample_conditions

Software:

NMRPipe v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.115, Goddard - data analysis

TALOS v+, Cornilescu, Delaglio and Bax - chemical shift calculation

X-PLOR NIH v2.24, Schwieters, Kuszewski, Tjandra and Clore - structure solution

REDCAT, Valafar and Prestegard - RDC analysis

PyMol, DeLano - structure analysis

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

BMRB	16237 17863
PDB	2KGS 2KSM 2L26
DBJ	BAH25212 BAL64801 BAQ04819 GAA44658
EMBL	CAL70937 CCC25980 CCC43237 CCC63509 CCE36433
GB	AAK45169 ABI54278 ABQ72638 ABR05261 ACT26182
REF	NP_215414 NP_854580 WP_003404684 WP_003915129 WP_014000491
SP	A1KH31 P65594 P9WIU4 P9WIU5
AlphaFold	A1KH31 P65594 P9WIU4 P9WIU5