3MDP

Crystal structure of a Putative Cyclic nucleotide-binding protein (Gmet_1532) from Geobacter metallireducens GS-15 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3MDP/pdb

• Classification: Nucleotide Binding Protein
• Organism(s): Geobacter metallireducens GS-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-30 Released: 2010-05-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal structure of a Putative Cyclic nucleotide-binding protein (Gmet_1532) from Geobacter metallireducens GS-15 at 1.90 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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.66 kDa 
• Atom Count: 1,214 
• Modelled Residue Count: 132 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic nucleotide-binding domain (CNMP-BD) protein	A	142	Geobacter metallireducens GS-15	Mutation(s): 0  Gene Names: Gmet_1532
UniProt
Find proteins for Q39VF8 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39VF8  Go to UniProtKB:  Q39VF8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	B [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 4 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33MDP

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.862	α = 90
b = 95.862	β = 90
c = 35.485	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations