2ZOM | pdb_00002zom

Crystal structure of CutA1 from Oryza sativa

• PDB DOI: https://doi.org/10.2210/pdb2ZOM/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-05-23 Released: 2009-05-26 
• Deposition Author(s): Kezuka, Y., Bagautdinov, B., Katoh, S., Ohtake, Y., Yutani, K., Nonaka, T., Katoh, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CutA1 from Oryza sativa

Kezuka, Y., Bagautdinov, B., Katoh, S., Ohtake, Y., Yutani, K., Nonaka, T., Katoh, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 38.18 kDa 
• Atom Count: 2,570 
• Modeled Residue Count: 324 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein CutA, chloroplast, putative, expressed	A, B, C	113	Oryza sativa Japonica Group	Mutation(s): 0
UniProt
Find proteins for Q109R6 (Oryza sativa subsp. japonica) Explore Q109R6  Go to UniProtKB:  Q109R6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], F [auth B], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.214	α = 90
b = 127.214	β = 90
c = 121.868	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Kezuka, Y., Bagautdinov, B., Katoh, S., Ohtake, Y., Yutani, K., Nonaka, T., Katoh, E.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description