1CQ6

ASPARTATE AMINOTRANSFERASE COMPLEX WITH C4-PYRIDOXAL-5P-PHOSPHATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Free energy requirement for domain movement of an enzyme

Ishijima, J., Nakai, T., Kawaguchi, S., Hirotsu, K., Kuramitsu, S.

(2000) J Biol Chem 275: 18939-18945

  • DOI: https://doi.org/10.1074/jbc.275.25.18939
  • Primary Citation of Related Structures:  
    1C9C, 1CQ6, 1CQ7, 1CQ8

  • PubMed Abstract: 

    Domain movement is sometimes essential for substrate recognition by an enzyme. X-ray crystallography of aminotransferase with a series of aliphatic substrates showed that the domain movement of aspartate aminotransferase was changed dramatically from an open to a closed form by the addition of only one CH(2) to the side chain of the C4 substrate CH(3)(CH(2))C((alpha))H(NH(3)(+))COO(-). These crystallographic results and reaction kinetics (Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55-63; Kawaguchi, S. and Kuramitsu, S. (1998) J. Biol. Chem. 273, 18353-18364) enabled us to estimate the free energy required for the domain movement.

    • Organizational Affiliation: 

    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan. Osaka 558-8585, Japan.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTATE AMINOTRANSFERASE396Escherichia coliMutation(s): 0 
EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12))
Explore P00509 
Go to UniProtKB:  P00509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00509
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PY4
Query on PY4
Download Ideal Coordinates CCD File 
B [auth A]2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID
C12 H19 N2 O7 P
VRMPGTOTVVJQMU-SNVBAGLBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.15α = 90
b = 86.32β = 90
c = 79.24γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations