1YDW | pdb_00001ydw

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT4G09670

• PDB DOI: https://doi.org/10.2210/pdb1YDW/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-26 Released: 2005-01-11 
• Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.283 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.226 (DCC) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4E

Literature

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT4G09670

Center for Eukaryotic Structural Genomics (CESG)

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: 79.69 kDa 
• Atom Count: 5,463 
• Modeled Residue Count: 693 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AX110P-like protein	A, B	362	Arabidopsis thaliana	Mutation(s): 6  Gene Names: At4g09670 EC: 1
UniProt
Find proteins for Q9SZ83 (Arabidopsis thaliana) Explore Q9SZ83  Go to UniProtKB:  Q9SZ83

Small Molecules

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: 2.49 Å
• R-Value Free:  0.283 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.226 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.197	α = 90
b = 107.663	β = 90
c = 129.748	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary