3E03 | pdb_00003e03

Crystal structure of a putative dehydrogenase from Xanthomonas campestris

PDB DOI: https://doi.org/10.2210/pdb3E03/pdb

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

Deposited: 2008-07-30 Released: 2008-09-16
Deposition Author(s): Sampathkumar, P., Wasserman, S., Rutter, M., Hu, S., Bain, K., Rodgers, L., Atwell, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.199 (Depositor), 0.164 (DCC)
R-Value Work:
0.161 (Depositor), 0.169 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3E03

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

Literature

Crystal structure of a putative dehydrogenase from Xanthomonas campestris

Sampathkumar, P., Wasserman, S., Rutter, M., Hu, S., Bain, K., Rodgers, L., Atwell, S., Sauder, J.M., Burley, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 86.1 kDa
Atom Count: 6,748
Modeled Residue Count: 810
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C	274	Xanthomonas campestris pv. campestris	Mutation(s): 0 Gene Names: XCC3285
UniProt
Find proteins for Q8P5Q1 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P5Q1 Go to UniProtKB: Q8P5Q1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8P5Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.199 (Depositor), 0.164 (DCC)
R-Value Work: 0.161 (Depositor), 0.169 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 251.286	α = 90
b = 41.351	β = 96.62
c = 73.323	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SHELXS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Sampathkumar, P.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-14
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, 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.