2OPL | pdb_00002opl

Crystal structure of an osmc-like protein (gsu2788) from geobacter sulfurreducens at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OPL/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Geobacter sulfurreducens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-29 Released: 2007-02-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal structure of hypothetical protein (NP_953832.1) from Geobacter sulfurreducens at 1.50 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)

Macromolecule Content 

• Total Structure Weight: 41.99 kDa 
• Atom Count: 3,504 
• Modeled Residue Count: 364 
• Deposited Residue Count: 374 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	187	Geobacter sulfurreducens	Mutation(s): 5  Gene Names: NP_953832.1, GSU2788
UniProt
Find proteins for Q749F5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q749F5  Go to UniProtKB:  Q749F5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	B	187	Geobacter sulfurreducens	Mutation(s): 5  Gene Names: NP_953832.1, GSU2788
UniProt
Find proteins for Q749F5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q749F5  Go to UniProtKB:  Q749F5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	E [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
MSE	A	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:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32OPL

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.24	α = 90
b = 83.01	β = 90
c = 95.45	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-02-13
  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: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary