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- PDB-1duv: CRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1duv
TitleCRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH NDELTA-L-ORNITHINE-DIAMINOPHOSPHINYL-N-SULPHONIC ACID (PSORN)
ComponentsORNITHINE TRANSCARBAMOYLASE
KeywordsTRANSFERASE / ENZYME-INHIBITOR COMPLEX
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline 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
NDELTA-(N'-SULPHODIAMINOPHOSPHINYL)-L-ORNITHINE / Ornithine carbamoyltransferase subunit I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsLangley, D.B. / Templeton, M.D. / Fields, B.A. / Mitchell, R.E. / Collyer, C.A.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Mechanism of inactivation of ornithine transcarbamoylase by Ndelta -(N'-Sulfodiaminophosphinyl)-L-ornithine, a true transition state analogue? Crystal structure and implications for catalytic mechanism.
Authors: Langley, D.B. / Templeton, M.D. / Fields, B.A. / Mitchell, R.E. / Collyer, C.A.
History
DepositionJan 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: ORNITHINE TRANSCARBAMOYLASE
H: ORNITHINE TRANSCARBAMOYLASE
I: ORNITHINE TRANSCARBAMOYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4457
Polymers110,4573
Non-polymers9894
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-26 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.680, 134.230, 109.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a trimer with one inhibitor molecule per monomer

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Components

#1: Protein ORNITHINE TRANSCARBAMOYLASE / OCTASE-1


Mass: 36818.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P04391, ornithine carbamoyltransferase
#2: Chemical ChemComp-PSQ / NDELTA-(N'-SULPHODIAMINOPHOSPHINYL)-L-ORNITHINE


Mass: 290.235 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H15N4O6PS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, PEG 1000, HEPES, DTT , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
217.8 %(w/v)PEG80001reservoir
32.2 %(w/v)PEG10001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 139550 / Num. obs: 119653 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.235 / Num. unique all: 4795 / % possible all: 34.7
Reflection shell
*PLUS
% possible obs: 34.7 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 6000 Random
Rwork0.192 --
all0.194 119618 -
obs0.194 119618 -
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7650 0 51 743 8444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5

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