3HIU | pdb_00003hiu

The crystal structure of protein (XCC3681) from Xanthomonas campestris pv. campestris str. ATCC 33913

PDB DOI: https://doi.org/10.2210/pdb3HIU/pdb

Classification: Structural Genomics, unknown function
Organism(s): Xanthomonas campestris pv. campestris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-20 Released: 2009-07-14
Deposition Author(s): Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.257 (Depositor), 0.254 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of protein (XCC3681) from Xanthomonas campestris pv. campestris str. ATCC 33913

Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.94 kDa
Atom Count: 5,066
Modeled Residue Count: 584
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	166	Xanthomonas campestris pv. campestris	Mutation(s): 0 Gene Names: XCC3681
UniProt
Find proteins for Q8P4M6 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P4M6 Go to UniProtKB: Q8P4M6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8P4M6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] K [auth B] F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], X [auth D], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], S [auth C], W [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain S [auth C] Focus chain W [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: 1.85 Å
R-Value Free: 0.257 (Depositor), 0.254 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.592	α = 90
b = 56.843	β = 90.01
c = 53.99	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary