3EZ1 | pdb_00003ez1

Crystal structure of putative aminotransferase (MocR family) (YP_604413.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 2.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EZ1/pdb

• Classification: TRANSFERASE
• Organism(s): Deinococcus geothermalis DSM 11300
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-22 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: 2.60 Å
• R-Value Free: 
  0.264 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of putative aminotransferase (MocR family) (YP_604413.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 2.60 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: 92.15 kDa 
• Atom Count: 6,503 
• Modeled Residue Count: 837 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase MocR family	A, B	423	Deinococcus geothermalis DSM 11300	Mutation(s): 0  Gene Names: YP_604413.1, Dgeo_0943
UniProt
Find proteins for Q1IZU0 (Deinococcus geothermalis (strain DSM 11300 / CIP 105573 / AG-3a)) Explore Q1IZU0  Go to UniProtKB:  Q1IZU0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 2.60 Å
• R-Value Free:  0.264 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EZ1

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.72	α = 90
b = 103.969	β = 112.63
c = 73.815	γ = 90

Software Package:

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

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: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection
• Version 1.7: 2024-11-20
  Changes: Structure summary