BMRB Entry 15190

Name: Solution Structure of Protein HP0495 from H. pylori; Northeast structural genomics consortium target PT2; Ontario Centre for Structural Proteomics target HP0488
Published: 2009-06-15

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PDB ID: 2joq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15190
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of Protein HP0495 from H. pylori; Northeast structural genomics consortium target PT2; Ontario Centre for Structural Proteomics target HP0488

Deposition date:

2007-03-19

Original release date:

2009-06-15

Authors:

Gutmanas, Aleksandras; Lemak, Alexander; Yee, Adelinda; Karra, Murthy; Srisailam, Sampath; Semesi, Anthony; Arrowsmith, Cheryl

Citation:

Citation: Gutmanas, Aleksandras; Lemak, Alexander; Yee, Adelinda; Karra, Murthy; Srisailam, Sampath; Semesi, Anthony; Arrowsmith, Cheryl. "Solution Structure of Protein HP0495 from H. pylori" The BMRB entry is the only known published source for the data..

Assembly members:

Assembly members:
HP0495, polymer, 91 residues, 10677.271 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 210 Superkingdom: Bacteria Kingdom: not available Genus/species: Helicobacter pylori

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: p11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HP0495: QGHMPSDSKKPTIIYPCLWD YRVIMTTKDTSTLKELLETY QRPFKLEFKNTSKNAKFYSF NVSMEVSNESERNEIFQKIS QLDKVVQTLGS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	413
15N chemical shifts	91
1H chemical shifts	653

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HP0495	1

Entities:

Entity 1, HP0495 91 residues - 10677.271 Da.

Residues 1-3 are from a non-native N-terminal affinity tag; Residues 90-91 are from non-native C-terminal affinity tag

1

GLN

GLY

HIS

MET

PRO

SER

ASP

SER

LYS

2

PRO

THR

ILE

TYR

PRO

CYS

LEU

TRP

ASP

3

TYR

ARG

VAL

ILE

MET

THR

LYS

ASP

THR

4

SER

THR

LEU

LYS

GLU

LEU

GLU

THR

TYR

5

GLN

ARG

PRO

PHE

LYS

LEU

GLU

PHE

LYS

ASN

6

THR

SER

LYS

ASN

ALA

LYS

PHE

TYR

SER

PHE

7

ASN

VAL

SER

MET

GLU

VAL

SER

ASN

GLU

SER

8

GLU

ARG

ASN

GLU

ILE

PHE

GLN

LYS

ILE

SER

9

GLN

LEU

ASP

LYS

VAL

GLN

THR

LEU

GLY

10

SER

Samples:

sample_1: HP0495, [U-13C; U-15N], 0.5 mM; TRIS 10 mM; sodium chloride 300 mM; benzamidine 1 mM; DTT 10 mM; sodium azide 0.01%; H2O 95%; D2O 5%

sample_2: HP0495, [U-13C; U-15N], 0.5 mM; TRIS 10 mM; sodium chloride 300 mM; benzamidine 1 mM; DTT 10 mM; sodium azide 0.01%; D2O 100%

sample_conditions_1: ionic strength: 300 mM; pH: 7; 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	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO sparse	sample_1	isotropic	sample_conditions_1
3D HNCA sparse	sample_1	isotropic	sample_conditions_1
3D H(CCCO)NH-TOCSY sparse	sample_1	isotropic	sample_conditions_1
3D (H)C(CCO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
4D HBHACBCA(CO)NH PR	sample_1	isotropic	sample_conditions_1
4D HC(CCO)NH-TOCSY PR	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY sparse	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D H(C)CH-TOCSY sparse	sample_2	isotropic	sample_conditions_1
3D (H)CCH-TOCSY sparse	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY sparse	sample_2	isotropic	sample_conditions_1
3D H(C)CH-TOCSY aromatic, sparse	sample_2	isotropic	sample_conditions_1
3D (H)CCH-TOCSY aromatic	sample_2	isotropic	sample_conditions_1
2D CT 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D CT 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1

Software:

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

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

SPARKY, Goddard - peak picking

TALOS, Cornilescu, Delaglio and Bax - dihedral angle constraints prediction

ABACUS, A. Lemak, A. Grishaev, M. Llinas, CH Arrowsmith - chemical shift and NOE assignment

MDD/MDDgui, A. Gutmanas, CH Arrowsmith, I Ibraghimov, V Yu Orekhov - processing of non-uniformly sampled data

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

PR, M Karra, CH Arrowsmith - processing of Projection-Reconstruction spectra

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 800 MHz
Varian INOVA 500 MHz

BMRB	15101
PDB	2H9Z 2JOQ
GB	AAD07569 ADU82921 AFV41714 AFV43308 AFV44901
REF	NP_207292 WP_001138777 WP_001138778
SP	O25237
AlphaFold	O25237