3LYH | pdb_00003lyh

Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LYH/pdb

Classification: LYASE
Organism(s): Marinobacter nauticus VT8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-26 Released: 2010-04-07
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.209 (Depositor), 0.220 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 28.27 kDa
Atom Count: 2,155
Modeled Residue Count: 242
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalamin (Vitamin B12) biosynthesis CbiX protein	A, B	126	Marinobacter nauticus VT8	Mutation(s): 0 Gene Names: Maqu_1136
UniProt
Find proteins for A1TZQ9 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8)) Explore A1TZQ9 Go to UniProtKB: A1TZQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1TZQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.209 (Depositor), 0.220 (DCC)
R-Value Work: 0.170 (Depositor), 0.180 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33LYH

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.836	α = 70.35
b = 38.615	β = 83.05
c = 39.845	γ = 72.09

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary

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.