3I0Y | pdb_00003i0y

Crystal structure of a putative polyketide cyclase (xcc0381) from xanthomonas campestris pv. campestris at 1.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb3I0Y/pdb

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

Deposited: 2009-06-25 Released: 2009-07-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.206 (Depositor), 0.212 (DCC)
R-Value Work:
0.169 (Depositor), 0.177 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative polyketide cyclase (NP_635776.1) from XANTHOMONAS CAMPESTRIS at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 64.28 kDa
Atom Count: 5,148
Modeled Residue Count: 545
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative polyketide cyclase	A, B, C, D	140	Xanthomonas campestris pv. campestris	Mutation(s): 0 Gene Names: NP_635776.1, XCC0381
UniProt
Find proteins for Q8PDF7 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PDF7 Go to UniProtKB: Q8PDF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PDF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth D]	G [auth A], K [auth B], L [auth B], Q [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] N [auth C] E [auth A], F [auth A], I [auth B], J [auth B], N [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	H [auth A], M [auth B], O [auth C], R [auth D]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [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: 1.50 Å
R-Value Free: 0.206 (Depositor), 0.212 (DCC)
R-Value Work: 0.169 (Depositor), 0.177 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.627	α = 90
b = 98.776	β = 110.45
c = 62.053	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Structure summary

3I0Y | pdb_00003i0y

Crystal structure of a putative polyketide cyclase (xcc0381) from xanthomonas campestris pv. campestris at 1.50 A resolution

Literature

Crystal structure of putative polyketide cyclase (NP_635776.1) from XANTHOMONAS CAMPESTRIS at 1.50 A resolution

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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