3I9S | pdb_00003i9s

Structure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6

PDB DOI: https://doi.org/10.2210/pdb3I9S/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-13 Released: 2009-08-11
Deposition Author(s): Deshpande, C.N., Sureshan, V., Harrop, S.J., Boucher, Y., Xu, X., Cui, H., Edwards, A., Savchenko, A., Joachimiak, A., Chang, C., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.233 (Depositor), 0.224 (DCC)
R-Value Work:
0.183 (Depositor), 0.177 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6

Deshpande, C.N., Sureshan, V., Harrop, S.J., Boucher, Y., G Curmi, P.M., Stokes, H.W., Edwards, A., Savchenko, A., Mabbutt, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 84.65 kDa
Atom Count: 5,451
Modelled Residue Count: 644
Deposited Residue Count: 732
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integron cassette protein	A, B, C, D	183	Vibrio cholerae	Mutation(s): 0 Gene Names: A59_A0465
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	E [auth A] F [auth A] H [auth B] J [auth C] K [auth C] E [auth A], F [auth A], H [auth B], J [auth C], K [auth C], L [auth C], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], I [auth B], M [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.233 (Depositor), 0.224 (DCC)
R-Value Work: 0.183 (Depositor), 0.177 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.239	α = 90
b = 75.239	β = 90
c = 310.424	γ = 90

Software Package:

Software Name	Purpose
ADSC	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: 2009-08-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary