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- PDB-1ort: ORNITHINE TRANSCARBAMOYLASE FROM PSEUDOMONAS AERUGINOSA -

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Basic information

Entry
Database: PDB / ID: 1ort
TitleORNITHINE TRANSCARBAMOYLASE FROM PSEUDOMONAS AERUGINOSA
ComponentsORNITHINE TRANSCARBAMOYLASE
KeywordsTRANSFERASE / ORNITHINE
Function / homology
Function and homology information


arginine deiminase pathway / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / arginine catabolic process to ornithine / amino acid binding / cytoplasm
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain ...Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ornithine carbamoyltransferase, catabolic
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsVilleret, V. / Dideberg, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of Pseudomonas aeruginosa catabolic ornithine transcarbamoylase at 3.0-A resolution: a different oligomeric organization in the transcarbamoylase family.
Authors: Villeret, V. / Tricot, C. / Stalon, V. / Dideberg, O.
History
DepositionAug 24, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORNITHINE TRANSCARBAMOYLASE
B: ORNITHINE TRANSCARBAMOYLASE
C: ORNITHINE TRANSCARBAMOYLASE
D: ORNITHINE TRANSCARBAMOYLASE
E: ORNITHINE TRANSCARBAMOYLASE
F: ORNITHINE TRANSCARBAMOYLASE
G: ORNITHINE TRANSCARBAMOYLASE
H: ORNITHINE TRANSCARBAMOYLASE
I: ORNITHINE TRANSCARBAMOYLASE
J: ORNITHINE TRANSCARBAMOYLASE
K: ORNITHINE TRANSCARBAMOYLASE
L: ORNITHINE TRANSCARBAMOYLASE


Theoretical massNumber of molelcules
Total (without water)455,49912
Polymers455,49912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: ORNITHINE TRANSCARBAMOYLASE
H: ORNITHINE TRANSCARBAMOYLASE
I: ORNITHINE TRANSCARBAMOYLASE


Theoretical massNumber of molelcules
Total (without water)113,8753
Polymers113,8753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-20 kcal/mol
Surface area39810 Å2
MethodPISA
3
B: ORNITHINE TRANSCARBAMOYLASE
F: ORNITHINE TRANSCARBAMOYLASE
J: ORNITHINE TRANSCARBAMOYLASE


Theoretical massNumber of molelcules
Total (without water)113,8753
Polymers113,8753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-20 kcal/mol
Surface area39810 Å2
MethodPISA
4
C: ORNITHINE TRANSCARBAMOYLASE
D: ORNITHINE TRANSCARBAMOYLASE
K: ORNITHINE TRANSCARBAMOYLASE


Theoretical massNumber of molelcules
Total (without water)113,8753
Polymers113,8753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-20 kcal/mol
Surface area39800 Å2
MethodPISA
5
A: ORNITHINE TRANSCARBAMOYLASE
E: ORNITHINE TRANSCARBAMOYLASE
L: ORNITHINE TRANSCARBAMOYLASE


Theoretical massNumber of molelcules
Total (without water)113,8753
Polymers113,8753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-20 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.360, 126.420, 134.540
Angle α, β, γ (deg.)85.07, 59.24, 111.97
Int Tables number1
Space group name H-MP1
DetailsTHE ORNITHINE CARBAMOYLTRANSFERASE IS A DODECAMER COMPOSED OF TWELVE MONOMERS RELATED BY THE 23 POINT GROUP SYMMETRY. THE DEPOSITOR PROVIDED COORDINATES CORRESPONDING TO ONE MONOMER. THE DODECAMER WAS GENERATED BY THE PDB USING THE NON-CRYSTALLOGRAPHIC SYMMETRY ROTATION MATRICES PROVIDED BY THE DEPOSITOR.

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Components

#1: Protein
ORNITHINE TRANSCARBAMOYLASE / ORNITHINE CARBAMOYLTRANSFERASE / OTCASE


Mass: 37958.250 Da / Num. of mol.: 12 / Mutation: E105G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / References: UniProt: P08308, ornithine carbamoyltransferase
Compound detailsTHE STRUCTURE IS NOT THE NATIVE ENZYME BUT A MUTANT FORM IN WHICH THE GLUTAMATE 105 HAS BEEN ...THE STRUCTURE IS NOT THE NATIVE ENZYME BUT A MUTANT FORM IN WHICH THE GLUTAMATE 105 HAS BEEN REPLACED BY A GLYCINE. THIS MUTANT IS BLOCKED IN THE R STATE CONFORMATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 60.04 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 mg/mlprotein1drop
250 mMHEPES1reservoir
350 %(w/v)ammonium sulfate1reservoir
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir
650 mMHEPES1drop

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 92630 / % possible obs: 85 % / Observed criterion σ(I): 3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Num. measured all: 116334

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
MADNESdata reduction
X-PLOR3phasing
RefinementResolution: 3→5.5 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.216 -
obs0.216 65411
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 3→5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31968 0 0 0 31968
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg4.01

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