1R0C | pdb_00001r0c

Products in the T State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-carbamyl-L-aspartate Ligated Enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.274 (Depositor) 
  • R-Value Work: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Products in the T-State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-Carbamyl-l-aspartate Ligated Enzyme

Huang, J.Lipscomb, W.N.

(2004) Biochemistry 43: 6422-6426

  • DOI: https://doi.org/10.1021/bi0302144
  • Primary Citation of Related Structures:  
    1R0C

  • PubMed Abstract: 

    The structure of aspartate transcarbamylase of Escherichia coli ligated to products (phosphate and N-carbamyl-l-aspartate) has been determined at 2.37 A resolution (R-factor = 0.23, R(free) = 0.27). Results might indicate a product release mode, rather than close analogues to the transition state like those found in our earlier studies of other ligands (N-phosphonacetyl-L-aspartate, carbamyl phosphate plus malonate, phosphonoacetamide plus malonate, or citrate plus phosphate). Ordered product release, first carbamylaspartate (CLA) and then phosphate, might be facilitated by a 4 A movement of phosphate from the substrate-analogue position to the product (phosphate) binding position, and by a somewhat similar release movement of the other product (CLA) relative to its analogue (citrate). This movement is consistent with earlier studies of binding of either pyrophosphate or phosphate alone [Honzatko, R. B., and Lipscomb, W. N. (1982) J. Mol. Biol. 160, 265-286].


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate carbamoyltransferase catalytic chainA,
C [auth G]
310Escherichia coliMutation(s): 0 
Gene Names: PYRB OR B4245 OR C5345 OR Z5856 OR ECS5222 OR SF4245 OR S4507
EC: 2.1.3.2
UniProt
Find proteins for P0A786 (Escherichia coli (strain K12))
Explore P0A786 
Go to UniProtKB:  P0A786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A786
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate carbamoyltransferase regulatory chainB,
D [auth H]
153Escherichia coliMutation(s): 0 
Gene Names: PYRI OR B4244 OR C5344 OR Z5855 OR ECS5221
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12))
Explore P0A7F3 
Go to UniProtKB:  P0A7F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7F3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.274 (Depositor) 
  • R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.776α = 90
b = 128.776β = 90
c = 198.017γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NCDClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description