1YBM | pdb_00001ybm

X-ray structure of selenomethionyl gene product from Arabidopsis thaliana at5g02240 in space group P21212

• PDB DOI: https://doi.org/10.2210/pdb1YBM/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-21 Released: 2005-01-18 
• Deposition Author(s): Wesenberg, G.E., Smith, D.W., 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: 2.10 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4B

Literature

X-ray structure of selenomethionyl gene product from Arabidopsis thaliana at5g02240 in space group P21212

Center for Eukaryotic Structural Genomics (CESG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.67 kDa 
• Atom Count: 4,137 
• Modeled Residue Count: 486 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown protein At5g02240	A, B	253	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At5g02240
UniProt
Find proteins for Q94EG6 (Arabidopsis thaliana) Explore Q94EG6  Go to UniProtKB:  Q94EG6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.634	α = 90
b = 77.286	β = 90
c = 92.864	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-02-01
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description