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- PDB-2otc: ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-O... -

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Basic information

Entry
Database: PDB / ID: 2otc
TitleORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-ORNITHINE
ComponentsORNITHINE CARBAMOYLTRANSFERASE
KeywordsTRANSFERASE / OTCASE / ORNITHINE / TRANSCARBAMOYLASE / ARGININE SYNTHESIS / UREA CYCLE
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
N-(PHOSPHONOACETYL)-L-ORNITHINE / Ornithine carbamoyltransferase subunit I
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHa, Y. / Allewell, N.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Substrate-induced conformational change in a trimeric ornithine transcarbamoylase.
Authors: Ha, Y. / McCann, M.T. / Tuchman, M. / Allewell, N.M.
History
DepositionJun 15, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE CARBAMOYLTRANSFERASE
B: ORNITHINE CARBAMOYLTRANSFERASE
C: ORNITHINE CARBAMOYLTRANSFERASE
D: ORNITHINE CARBAMOYLTRANSFERASE
E: ORNITHINE CARBAMOYLTRANSFERASE
F: ORNITHINE CARBAMOYLTRANSFERASE
G: ORNITHINE CARBAMOYLTRANSFERASE
H: ORNITHINE CARBAMOYLTRANSFERASE
I: ORNITHINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,28818
Polymers332,0019
Non-polymers2,2889
Water6,161342
1
A: ORNITHINE CARBAMOYLTRANSFERASE
B: ORNITHINE CARBAMOYLTRANSFERASE
C: ORNITHINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4296
Polymers110,6673
Non-polymers7633
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-12 kcal/mol
Surface area34300 Å2
MethodPISA
2
D: ORNITHINE CARBAMOYLTRANSFERASE
E: ORNITHINE CARBAMOYLTRANSFERASE
F: ORNITHINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4296
Polymers110,6673
Non-polymers7633
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-12 kcal/mol
Surface area34280 Å2
MethodPISA
3
G: ORNITHINE CARBAMOYLTRANSFERASE
H: ORNITHINE CARBAMOYLTRANSFERASE
I: ORNITHINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4296
Polymers110,6673
Non-polymers7633
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-13 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.030, 114.690, 93.780
Angle α, β, γ (deg.)86.99, 93.11, 118.81
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.491485, -0.323452, 0.808592), (0.16914, 0.87534, 0.45296), (-0.854303, 0.359388, -0.375508)5.0134, -17.384, 59.9344
2given(-0.500611, 0.17919, -0.846923), (-0.326, 0.867295, 0.376196), (0.801943, 0.464425, -0.375762)55.7815, -4.8444, 25.7847
3given(-0.502788, 0.856027, -0.12009), (-0.863338, -0.504211, 0.020464), (-0.043033, 0.113967, 0.992552)50.6518, 126.2208, 29.8148
4given(0.48172, 0.875212, 0.04415), (0.32853, -0.133659, -0.934988), (-0.812412, 0.464908, -0.35192)25.0807, 130.79761, 87.3221
5given(-0.12933, 0.608696, 0.782791), (0.605679, -0.576555, 0.548395), (0.785128, 0.545045, -0.294109)15.2199, 80.2781, 52.7466
6given(-0.512685, -0.857224, -0.048172), (0.85423, -0.514925, 0.071714), (-0.086279, -0.004383, 0.996261)128.4445, 11.4168, -30.4104
7given(0.153948, -0.596352, -0.787823), (-0.56609, -0.706732, 0.42435), (-0.809841, 0.380651, -0.446388)137.47591, 29.5266, 29.0635
8given(0.496235, -0.857695, 0.134577), (-0.196833, -0.262118, -0.944749), (0.845582, 0.442328, -0.298894)102.4937, 63.5039, -9.67

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Components

#1: Protein
ORNITHINE CARBAMOYLTRANSFERASE / OTCASE / L-ORNITHINE CARBAMOYL PHOSPHATE TRANSFERASE


Mass: 36888.953 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: N-(PHOSPHONACETYL)-L-ORNITHINE / Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21 (DE3) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: ARGI / Plasmid: PET-ARGI / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): ARGI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04391, ornithine carbamoyltransferase
#2: Chemical
ChemComp-PAO / N-(PHOSPHONOACETYL)-L-ORNITHINE


Mass: 254.178 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H15N2O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.9 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.5
Details: 14% PEG 4K, 90MM NA ACETATE, 70MM MGCL2, 2% MPD, 45% TRIS-HCL PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
21 mg/mlPALO1drop
310 mMHEPES1drop
414 %PEG33501reservoir
590 mMsodium acetate1reservoir
670 mM1reservoirMgCl2
72 %MPD1reservoir
845 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1997 / Details: NO
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 53778 / % possible obs: 58 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 9.73 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.13 / Net I/σ(I): 7
Reflection shellResolution: 2.8→3 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.262 / Rsym value: 0.208 / % possible all: 20
Reflection shell
*PLUS
% possible obs: 20 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTC

1otc


Resolution: 2.8→15 Å / Data cutoff high absF: 40 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.23 5000 10 %RANDOM
Rwork0.213 ---
obs0.213 50112 58 %-
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 16 38 2633
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.664
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.202
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
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 156 10.3 %
Rwork0.327 1352 -
obs--17 %
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.202
LS refinement shell
*PLUS
Rfactor obs: 0.327

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