3EY7 | pdb_00003ey7

Structure from the mobile metagenome of V. Cholerae. Integron cassette protein VCH_CASS1

PDB DOI: https://doi.org/10.2210/pdb3EY7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-10-20 Released: 2009-01-13
Deposition Author(s): Harrop, S.J., Deshpande, C.N., Sureshan, V., Boucher, Y., Xu, X., Cui, H., Chang, C., Edwards, A., Joachimiak, A., Savchenko, A., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.216 (Depositor), 0.210 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure from the mobile metagenome of V. Cholerae. Integron cassette protein VCH_CASS1

Harrop, S.J., Deshpande, C.N., Sureshan, V., Boucher, Y., Xu, X., Cui, H., Chang, C., Edwards, A., Joachimiak, A., Savchenko, A., Curmi, P.M.G., Mabbutt, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 29.79 kDa
Atom Count: 2,515
Modelled Residue Count: 260
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biphenyl-2,3-diol 1,2-dioxygenase III-related protein	A, B	133	Vibrio cholerae	Mutation(s): 1 Gene Names: VC_A0328, VC_A0341, VC_A0463
UniProt
Find proteins for Q9K3D3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9K3D3 Go to UniProtKB: Q9K3D3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K3D3
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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: 0.216 (Depositor), 0.210 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.029	α = 90
b = 67.868	β = 90
c = 91.24	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Deshpande, C.N.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-12-27
Changes: Data collection
Version 1.4: 2024-10-30
Changes: 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.