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- PDB-1fvo: CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1fvo
TitleCRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASE COMPLEXED WITH CARBAMOYL PHOSPHATE
ComponentsORNITHINE TRANSCARBAMYLASE
KeywordsTRANSFERASE / Two domains / alpha/beta topology
Function / homology
Function and homology information


response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import ...response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import / urea cycle / midgut development / amino acid binding / response to zinc ion / 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 / SYNCHROTRON / Resolution: 2.6 Å
AuthorsShi, D. / Morizono, H. / Yu, X. / Allewell, N.M. / Tuchman, M.
Citation
Journal: 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.
#1: Journal: Proteins / Year: 2000
Title: Crystal Structure of Human Ornithine Transcarbamylase Complexed with Carbamoyl Phosphate and L-norvaline at 1.9 A Resolution
Authors: Shi, D. / Morizono, H. / Aoyagi, M. / Tuchman, M. / Allewell, N.M.
History
DepositionSep 20, 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 1.3Dec 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 1.4May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4954
Polymers72,2132
Non-polymers2822
Water77543
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 operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area7730 Å2
ΔGint-61 kcal/mol
Surface area36020 Å2
MethodPISA, PQS
2
B: ORNITHINE TRANSCARBAMYLASE
hetero molecules

B: ORNITHINE TRANSCARBAMYLASE
hetero molecules

B: 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 operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area7660 Å2
ΔGint-65 kcal/mol
Surface area36020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)203.426, 203.426, 203.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsThe biological assembly is a trimer constructed from chain A or chain B by symmetry partners generated by the three-fold.

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Components

#1: Protein ORNITHINE TRANSCARBAMYLASE / OTCASE


Mass: 36106.551 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4

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Sample preparation

CrystalDensity Matthews: 4.86 Å3/Da / Density % sol: 74.67 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: Mes, PEG 8000, pH 6.5, EVAPORATION, temperature 291.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMes1reservoir
216 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 300506 / Num. obs: 42459 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.76 Å / Rmerge(I) obs: 0.029 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 300506
Reflection shell
*PLUS
% possible obs: 94.1 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
GLRFphasing
CNS1refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.6→29.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6208044.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2090 5 %RANDOM
Rwork0.202 ---
all0.204 41624 --
obs0.202 41624 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.33 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 16 43 5133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 342 5.1 %
Rwork0.304 6338 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CP.PARAMCP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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