2Q30

Crystal structure of a rmlc-like cupin protein (dde_2303) from desulfovibrio desulfuricans subsp. at 1.94 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2Q30/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Oleidesulfovibrio alaskensis G20
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-29 Released: 2007-06-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.212 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Crystal structure of uncharacterized protein (YP_388795.1) from Desulfovibrio desulfuricans G20 at 1.94 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.76 kDa 
• Atom Count: 7,119 
• Modelled Residue Count: 838 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F, G, H	110	Oleidesulfovibrio alaskensis G20	Mutation(s): 4  Gene Names: YP_388795.1, Dde_2303
UniProt
Find proteins for Q30YZ6 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q30YZ6  Go to UniProtKB:  Q30YZ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth A], J [auth B], K [auth C], M [auth D], N [auth E], O [auth F], P [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.212 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M32Q30

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.14	α = 90
b = 133.95	β = 93.04
c = 74.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations