4LGQ | pdb_00004lgq

Crystal structure of a putative polyketide cyclase (CV_0247) from Chromobacterium violaceum ATCC 12472 at 2.72 A resolution

PDB DOI: https://doi.org/10.2210/pdb4LGQ/pdb

Classification: LYASE
Organism(s): Chromobacterium violaceum ATCC 12472
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-28 Released: 2013-07-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.219 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative polyketide cyclase (CV_0247) from Chromobacterium violaceum ATCC 12472 at 2.72 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 62.16 kDa
Atom Count: 4,245
Modeled Residue Count: 536
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative polyketide cyclase	A, B, C, D	140	Chromobacterium violaceum ATCC 12472	Mutation(s): 0 Gene Names: CV_0247
UniProt
Find proteins for Q7P1G6 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7P1G6 Go to UniProtKB: Q7P1G6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7P1G6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A], K [auth C], L [auth C], O [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], M [auth C], P [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B]	G [auth B], J [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth C] Focus chain N [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: 2.72 Å
R-Value Free: 0.219 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34LGQ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.1	α = 90
b = 98.076	β = 90
c = 104.958	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement