4Z48 | pdb_00004z48

Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4Z48/pdb

• Classification: Structural Biology, Unknown Function
• Organism(s): Desulfovibrio piger ATCC 29098
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-01 Released: 2015-04-22 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.01 kDa 
• Atom Count: 4,552 
• Modeled Residue Count: 480 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	246	Desulfovibrio piger ATCC 29098	Mutation(s): 0  Gene Names: DESPIG_00262
UniProt
Find proteins for B6WQE2 (Desulfovibrio piger ATCC 29098) Explore B6WQE2  Go to UniProtKB:  B6WQE2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
IOD	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	F [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.75 Å
• R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3HC71

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.4	α = 100.71
b = 56.34	β = 97.04
c = 65.56	γ = 109.01

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER	refinement
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary