1XI9

Alanine aminotransferase from Pyrococcus furiosus Pfu-1397077-001

• PDB DOI: https://doi.org/10.2210/pdb1XI9/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-21 Released: 2004-11-23 
• Deposition Author(s): Zhou, W., Tempel, W., Shah, A., Chen, L., Liu, Z.-J., Lee, D., Lin, D., Chang, S.-H., Brereton, P.S., Izumi, M., Jenney Jr., F.E., Lee, H.-S., Poole II, F.L., Shah, C., Sugar, F.J., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Adams, M.W.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Alanine aminotransferase from Pyrococcus furiosus Pfu-1397077-001

Zhou, W., Tempel, W., Shah, A., Chen, L., Liu, Z.-J., Lee, D., Lin, D., Chang, S.-H., Brereton, P.S., Izumi, M., Jenney Jr., F.E., Lee, H.-S., Poole II, F.L., Shah, C., Sugar, F.J., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Adams, M.W.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 186.23 kDa 
• Atom Count: 12,327 
• Modelled Residue Count: 1,553 
• Deposited Residue Count: 1,624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative transaminase	A, B, C, D	406	Pyrococcus furiosus DSM 3638	Mutation(s): 0
UniProt
Find proteins for Q9P9M8 (Pyrococcus furiosus) Explore Q9P9M8  Go to UniProtKB:  Q9P9M8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.804	α = 90
b = 188.089	β = 89.79
c = 72.583	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-23 
Deposition Author(s): Zhou, W., Tempel, W., Shah, A., Chen, L., Liu, Z.-J., Lee, D., Lin, D., Chang, S.-H., Brereton, P.S., Izumi, M., Jenney Jr., F.E., Lee, H.-S., Poole II, F.L., Shah, C., Sugar, F.J., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Adams, M.W.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description