4R7K | pdb_00004r7k

1.88 Angstrom Resolution Crystal Structure of Hypothetical Protein jhp0584 from Helicobacter pylori.

PDB DOI: https://doi.org/10.2210/pdb4R7K/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Helicobacter pylori J99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-27 Released: 2014-09-10
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.207 (Depositor), 0.215 (DCC)
R-Value Work:
0.171 (Depositor), 0.183 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4R7K

This is version 1.2 of the entry. See complete history.

Literature

1.88 Angstrom Resolution Crystal Structure of Hypothetical Protein jhp0584 from Helicobacter pylori.

Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 90.22 kDa
Atom Count: 6,110
Modeled Residue Count: 672
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein jhp0584	A, B, C, D	191	Helicobacter pylori J99	Mutation(s): 0 Gene Names: jhp0584, jhp_0584
UniProt
Find proteins for Q9ZLJ5 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZLJ5 Go to UniProtKB: Q9ZLJ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZLJ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.207 (Depositor), 0.215 (DCC)
R-Value Work: 0.171 (Depositor), 0.183 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.832	α = 90
b = 70.945	β = 91.67
c = 86.454	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.