3EZU | pdb_00003ezu

Crystal structure of multidomain protein of unknown function with GGDEF-domain (NP_951600.1) from GEOBACTER SULFURREDUCENS at 1.95 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EZU/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Geobacter sulfurreducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-23 Released: 2008-11-18 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of multidomain protein of unknown function with GGDEF-domain (NP_951600.1) from GEOBACTER SULFURREDUCENS at 1.95 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: 38.28 kDa 
• Atom Count: 2,819 
• Modeled Residue Count: 336 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF domain protein	A	342	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: NP_951600.1, GSU0542 EC: 2.7.7.65
UniProt
Find proteins for Q74FR4 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74FR4  Go to UniProtKB:  Q74FR4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	B [auth A]	Unknown ligand 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: 1.95 Å
• R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EZU

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.55	α = 90
b = 76.367	β = 90
c = 64.191	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary