1VRB | pdb_00001vrb

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VRB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-02-18 Released: 2005-03-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.221 (Depositor), 0.224 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 157.36 kDa
Atom Count: 9,036
Modeled Residue Count: 1,224
Deposited Residue Count: 1,368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative asparaginyl hydroxylase	A, B, C, D	342	Bacillus subtilis	Mutation(s): 6 Gene Names: yxbC
UniProt
Find proteins for P46327 (Bacillus subtilis (strain 168)) Explore P46327 Go to UniProtKB: P46327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 2.60 Å
R-Value Free: 0.272 (Depositor), 0.272 (DCC)
R-Value Work: 0.221 (Depositor), 0.224 (DCC)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.3	α = 90
b = 104.66	β = 90
c = 286.61	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELXD	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
autoSHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-03-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-15
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, Refinement description, 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.