3G2B | pdb_00003g2b

crystal structure of PqqD from xanthomonas campestris

PDB DOI: https://doi.org/10.2210/pdb3G2B/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Xanthomonas campestris pv. campestris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-31 Released: 2009-09-01
Deposition Author(s): Yang, C.-Y., Tsai, T.-Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 3G2B

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

Literature

Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle-like fold that possibly serves as a PQQ carrier

Tsai, T.-Y., Yang, C.-Y., Shih, H.-L., Wang, A.H.-J., Chou, S.-H.

(2009) Proteins 76: 1042-1048

PubMed: 19475705 Search on PubMed
DOI: https://doi.org/10.1002/prot.22461
Primary Citation Related Structures:
3G2B

Organizational Affiliation

Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227, Taiwan, Republic of China.

Macromolecule Content

Total Structure Weight: 10.68 kDa
Atom Count: 817
Modeled Residue Count: 90
Deposited Residue Count: 95
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme PQQ synthesis protein D	A	95	Xanthomonas campestris pv. campestris	Mutation(s): 0 Gene Names: pqqD
UniProt
Find proteins for Q8P6M8 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P6M8 Go to UniProtKB: Q8P6M8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8P6M8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.228 (Depositor), 0.227 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.9	α = 90
b = 66.25	β = 90
c = 93.88	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.