BMRB Entry 15821

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PDB ID: 2k52
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15821
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:

Structure of uncharacterized protein MJ1198 from Methanocaldococcus jannaschii. Northeast Structural Genomics Target MjR117B

Deposition date:

2008-06-24

Original release date:

2008-07-15

Authors:

Rossi, Paolo; Maglaqui, Melissa; Foote, Erica; Hamilton, Keith; Ciccosanti, Coleen; Xiao, Rong; Nair, Rajesh; Swapna, G.V.T.; Everett, John; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano

Citation:

Citation: Rossi, Paolo; Xiao, Rong; Acton, Thomas; Montelione, Gaetano. "Structure of uncharacterized protein MJ1198 from Methanocaldococcus jannaschii. Northeast Structural Genomics Target MjR117B" .

Assembly members:

Assembly members:
MjR117B, polymer, 74 residues, 8674.141 Da.

Natural source:

Natural source: Common Name: Methanococcus jannaschii Taxonomy ID: 2190 Superkingdom: Archaea Kingdom: not available Genus/species: Methanococcus jannaschii

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET 21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MjR117B: MDVEPGKFYKGVVTRIEKYG AFINLNEQVRGLLRPRDMIS LRLENLNVGDEIIVQAIDVR PEKREIDFKYIPLE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	346
15N chemical shifts	75
1H chemical shifts	566

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MJ1198	1

Entities:

Entity 1, MJ1198 74 residues - 8674.141 Da.

N-term M is a cloning artifact and the C-term LE is part of the purification tag

1

MET

ASP

VAL

GLU

PRO

GLY

LYS

PHE

TYR

LYS

2

GLY

VAL

THR

ARG

ILE

GLU

LYS

TYR

GLY

3

ALA

PHE

ILE

ASN

LEU

ASN

GLU

GLN

VAL

ARG

4

GLY

LEU

ARG

PRO

ARG

ASP

MET

ILE

SER

5

LEU

ARG

LEU

GLU

ASN

LEU

ASN

VAL

GLY

ASP

6

GLU

ILE

VAL

GLN

ALA

ILE

ASP

VAL

ARG

7

PRO

GLU

LYS

ARG

GLU

ILE

ASP

PHE

LYS

TYR

8

ILE

PRO

LEU

GLU

Samples:

sample_1: MjR117B, [U-100% 13C; U-100% 15N], 1.682 mM; ammonium acetate 20 mM; sodium chloride 100 mM; sodium azide 0.02 mM; DTT 10 mM; DSS 50 uM; calcium chloride 5 mM; protease inhibitor 1x mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_2: MjR117B, [5% 13C; U-100% 15N], 1.226 mM; ammonium acetate 20 mM; sodium chloride 100 mM; sodium azide 0.02 mM; DTT 10 mM; DSS 50 uM; calcium chloride 5 mM; protease inhibitor 1x mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 4.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC (aliph)	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D SIM 13C,15N NOESY	sample_1	isotropic	sample_conditions_1
3D ARO 13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC Stereo	sample_2	isotropic	sample_conditions_1
2D HETNOE	sample_2	isotropic	sample_conditions_1
pseudo 2D N15 T1	sample_2	isotropic	sample_conditions_1
pseudo 2D N15 T2 (CPMG)	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC CT ARO	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

SPARKY v3.113, Goddard - data analysis

TOPSPIN v2.1, Bruker Biospin - collection

RPF(AutoStructure) v2.2.1, Huang, Tejero, Powers and Montelione - validation

PSVS v1.3, Bhattacharya and Montelione - validation

Molmol, Koradi, Billeter and Wuthrich - visualization

Procheck, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - validation

MolProbity, Richardson - validation

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	2K52
GB	AAB99202 ACV24909 ADC69513 AIJ05492
REF	WP_012980423 WP_015791645 WP_048201674
SP	Q58598
AlphaFold	Q58598