5VRD | pdb_00005vrd

Crystal structure for Methylobacterium extorquens PqqCD (natural fusion)

PDB DOI: https://doi.org/10.2210/pdb5VRD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methylorubrum extorquens AM1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-05-10 Released: 2018-05-16
Deposition Author(s): Evans III, R.L., Wilmot, C.M., Esler, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.327 (Depositor), 0.328 (DCC)
R-Value Work:
0.253 (Depositor), 0.255 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5VRD

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures for Methylobacterium extorquens PqqC from the CD natural fusion and the C truncation

Evans III, R.L., Esler, M.A., Latham, J.A., Klinman, J.P., Wilmot, C.M.

Not Published

Macromolecule Content

Total Structure Weight: 175.21 kDa
Atom Count: 6,570
Modeled Residue Count: 815
Deposited Residue Count: 1,568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional coenzyme PQQ synthesis protein C/D	A [auth D], B [auth A], C [auth B], D [auth C]	392	Methylorubrum extorquens AM1	Mutation(s): 0 Gene Names: pqqCD, MexAM1_META1p1749 EC: 1.3.3.11
UniProt
Find proteins for Q49150 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore Q49150 Go to UniProtKB: Q49150
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q49150
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.327 (Depositor), 0.328 (DCC)
R-Value Work: 0.253 (Depositor), 0.255 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.936	α = 90
b = 103.936	β = 90
c = 243.485	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Evans III, R.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-66569 (C.M.W.)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-118117 (J.P.K.)

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2019-05-29
Changes: Data collection, Database references
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.