2O8Q | pdb_00002o8q

CRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN FUNCTION (BXE_C0505) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.55 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2O8Q/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-12 Released: 2006-12-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of hypothetical protein (YP_555756.1) from Burkholderia xenovorans LB400 at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 30.79 kDa 
• Atom Count: 2,261 
• Modeled Residue Count: 244 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	134	Paraburkholderia xenovorans LB400	Mutation(s): 3  Gene Names: YP_555756.1
UniProt
Find proteins for Q13HN3 (Paraburkholderia xenovorans (strain LB400)) Explore Q13HN3  Go to UniProtKB:  Q13HN3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	C [auth A], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32O8Q

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.255	α = 90
b = 102.255	β = 90
c = 74.746	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary