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- PDB-1akm: ORNITHINE TRANSCARBAMYLASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1akm
TitleORNITHINE TRANSCARBAMYLASE FROM ESCHERICHIA COLI
ComponentsORNITHINE TRANSCARBAMYLASE
KeywordsTRANSFERASE / ANABOLIC / UREA CYCLE / CARBAMYL PHOSPHATE
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / amino acid binding / metal ion 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 subunit I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, SIRAS / Resolution: 2.8 Å
AuthorsHead, J.F. / Seaton, B. / Jin, L.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure at 2.8 A resolution of anabolic ornithine transcarbamylase from Escherichia coli.
Authors: Jin, L. / Seaton, B.A. / Head, J.F.
History
DepositionMay 23, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 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 TRANSCARBAMYLASE
B: ORNITHINE TRANSCARBAMYLASE
C: ORNITHINE TRANSCARBAMYLASE


Theoretical massNumber of molelcules
Total (without water)110,4573
Polymers110,4573
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-26 kcal/mol
Surface area33940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.600, 104.600, 86.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6006, -0.7946, -0.0886), (-0.2181, -0.2694, 0.938), (-0.7692, -0.544, -0.3351)56.9159, 58.4109, 76.4341
2given(0.6141, -0.2493, -0.7489), (-0.7873, -0.2598, -0.5591), (-0.0552, 0.9329, -0.3558)38.6478, 101.9194, -24.3479

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Components

#1: Protein ORNITHINE TRANSCARBAMYLASE / ORNITHINE CARBAMOYLTRANSFERASE / ORNITHINE TRANSCARBAMOYLASE


Mass: 36818.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARGI / Plasmid: PUC18 / Gene (production host): ARGI / Production host: Escherichia coli (E. coli) / Strain (production host): TB2 / Variant (production host): DELTA ARGI-PYRB, ARGF- / References: UniProt: P04391, ornithine carbamoyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5
Details: CRYSTALLIZED FROM 20% PEG 4000, 10% MPD, 1MM MGSO4, 50MM HEPES, PH 7.5.
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 %beta-octyl glucoside11
218 %(w/v)PEG11
310 %(v/v)MPD11
41 mM11MgSO4
520 mMHEPES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→90 Å / Num. obs: 25858 / % possible obs: 98.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SIRAS
Starting model: PDB ENTRY 2AT2

2at2


Resolution: 2.8→6 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 -10 %RANDOM
Rwork0.229 ---
obs0.229 20993 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 0 0 7482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS

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