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- PDB-1ep9: HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO ... -

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Basic information

Entry
Database: PDB / ID: 1ep9
TitleHUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE
ComponentsORNITHINE TRANSCARBAMYLASE
KeywordsTRANSFERASE / protein-substrate complex
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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Ornithine transcarbamylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsShi, D. / Morizono, H. / Yu, X. / Allewell, N.M. / Tuchman, M.
CitationJournal: Biochem.J. / Year: 2001
Title: Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes.
Authors: Shi, D. / Morizono, H. / Yu, X. / Tong, L. / Allewell, N.M. / Tuchman, M.
History
DepositionMar 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 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 TRANSCARBAMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2482
Polymers36,1071
Non-polymers1411
Water2,864159
1
A: ORNITHINE TRANSCARBAMYLASE
hetero molecules

A: ORNITHINE TRANSCARBAMYLASE
hetero molecules

A: ORNITHINE TRANSCARBAMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7436
Polymers108,3203
Non-polymers4233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8050 Å2
ΔGint-62 kcal/mol
Surface area35270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.60, 125.60, 125.60
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a trimer constructed from chain A a symmetry partner generated by the three-fold.

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Components

#1: Protein ORNITHINE TRANSCARBAMYLASE / OTCASE


Mass: 36106.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / References: UniProt: P00480, ornithine carbamoyltransferase
#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20 MM TRISAC, 2MM EDTA, 20MM KCL, 4MM PALO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 73 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 333653 / Num. obs: 26061 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.3
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.402 / Num. unique all: 4070 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 333653
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
X-GENdata reduction
X-GENdata scaling
RefinementResolution: 2.4→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1884 -RANDOM
Rwork0.184 ---
all-26061 --
obs-22885 87.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 8 159 2695
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg2.61
X-RAY DIFFRACTIONx_dihedral_angle_d23.98
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.219

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