1YVI | pdb_00001yvi

X-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN FROM RICE, AK104879

• PDB DOI: https://doi.org/10.2210/pdb1YVI/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Oryza sativa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-15 Released: 2005-02-22 
• 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: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4F

Literature

X-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN FROM RICE, AK104879

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: 33.56 kDa 
• Atom Count: 2,502 
• Modeled Residue Count: 276 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine-containing phosphotransfer protein	A, B	149	Oryza sativa	Mutation(s): 0  Gene Names: AK104879
UniProt
Find proteins for Q6VAK4 (Oryza sativa subsp. japonica) Explore Q6VAK4  Go to UniProtKB:  Q6VAK4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.558	α = 90
b = 100.558	β = 90
c = 69.568	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
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: 2005-02-22
  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: 2018-01-24
  Changes: Database references
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description