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- PDB-1oth: CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1oth
TitleCRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ORNITHINE
ComponentsPROTEIN (ORNITHINE TRANSCARBAMOYLASE)
KeywordsTRANSFERASE / TRANSCARBAMOYLASE
Function / homology
Function and homology information


response to biotin / L-ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine ...response to biotin / L-ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / urea cycle / Mitochondrial protein import / L-arginine biosynthetic process / response to zinc ion / amino acid binding / phosphate ion binding / liver development / response to insulin / phospholipid binding / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / identical protein binding
Similarity search - Function
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 ...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 transcarbamylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShi, D. / Morizono, H. / Ha, Y. / Aoyagi, M. / Tuchman, N. / Allewell, N.M.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: 1.85-A resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-L-ornithine. Catalytic mechanism and correlation with inherited deficiency.
Authors: Shi, D. / Morizono, H. / Ha, Y. / Aoyagi, M. / Tuchman, M. / Allewell, N.M.
History
DepositionOct 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Aug 16, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PROTEIN (ORNITHINE TRANSCARBAMOYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3612
Polymers36,1071
Non-polymers2541
Water3,873215
1
A: PROTEIN (ORNITHINE TRANSCARBAMOYLASE)
hetero molecules

A: PROTEIN (ORNITHINE TRANSCARBAMOYLASE)
hetero molecules

A: PROTEIN (ORNITHINE TRANSCARBAMOYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0826
Polymers108,3203
Non-polymers7633
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6900 Å2
ΔGint-36 kcal/mol
Surface area34610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.900, 125.900, 125.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

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Components

#1: Protein PROTEIN (ORNITHINE TRANSCARBAMOYLASE)


Mass: 36106.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-PHOSPHONACETYL-L-ORNITHINE BIND ACTIVE SITE / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETOTCII / Production host: Escherichia coli (E. coli) / References: UniProt: P00480
#2: Chemical ChemComp-PAO / N-(PHOSPHONOACETYL)-L-ORNITHINE


Mass: 254.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N2O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 4.8 Å3/Da / Density % sol: 73 %
Crystal growpH: 7.5
Details: 20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO PH=7.4, pH 7.5
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlOTCase1drop
24 mMPALO1drop
320 mMTris-acetate1drop
42 mMEDTA1drop
520 mM1dropKCl
62 %PEG4001reservoir
72 Mammonium sulfate1reservoir
80.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorDate: Mar 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 51424 / % possible obs: 86.4 % / Observed criterion σ(I): 1 / Redundancy: 28 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.2
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 25 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.4 / % possible all: 63.3
Reflection
*PLUS
Num. measured all: 1393080
Reflection shell
*PLUS
% possible obs: 63.3 % / Num. unique obs: 51424 / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ORT

2ort


Resolution: 1.85→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.201 -10 %RANDOM
Rwork0.179 ---
obs0.179 48218 85.6 %-
Displacement parametersBiso mean: 17.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 16 215 2764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.877
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
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.251 -8.6 %
Rwork0.243 3248 -
obs--55.1 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.877
LS refinement shell
*PLUS
Rfactor Rfree: 0.251 / % reflection Rfree: 8.6 % / Rfactor Rwork: 0.243 / Rfactor obs: 0.243

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