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
Modeled Residue Count: 644
Deposited Residue Count: 732
Unique protein chains: 1

Macromolecules

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| 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

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

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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