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- PDB-1pvv: Refined Structure of Pyrococcus furiosus Ornithine Carbamoyltrans... -

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Basic information

Entry
Database: PDB / ID: 1pvv
TitleRefined Structure of Pyrococcus furiosus Ornithine Carbamoyltransferase at 1.87 A
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / dodecamer
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 / 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
Ornithine carbamoyltransferase, anabolic
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.87 Å
AuthorsMassant, J. / Wouters, J. / Glansdorff, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87 A.
Authors: Massant, J. / Wouters, J. / Glansdorff, N.
History
DepositionJun 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4223
Polymers35,2291
Non-polymers1922
Water3,441191
1
A: Ornithine carbamoyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)425,05836
Polymers422,75312
Non-polymers2,30624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area48180 Å2
ΔGint-414 kcal/mol
Surface area111080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)184.777, 184.777, 184.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

21A-402-

SO4

31A-1024-

HOH

41A-1033-

HOH

51A-1065-

HOH

61A-1094-

HOH

71A-1159-

HOH

81A-1187-

HOH

DetailsThe biological assembly is a dodecamer generated from the monomer in the asymmetric unit

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Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 35229.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: ARGF OR PF0594 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q51742, ornithine carbamoyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.23 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, ammonium sulfate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.08 Msodium acetate1reservoirpH4.6
22.4 Mammonium sulfate1reservoir
320 %glycerol1reservoir
48.3 mg/mlPfu OTCase1drop
51.7 mg/mlPfu CKase1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.989 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.87→99 Å / Num. all: 42928 / Num. obs: 42928 / % possible obs: 98.5 % / Rmerge(I) obs: 0.033
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.187 / % possible all: 86.5
Reflection
*PLUS
Num. measured all: 304009
Reflection shell
*PLUS
% possible obs: 86.5 %

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1A1S

1a1s


Resolution: 1.87→99 Å / Num. parameters: 10575 / Num. restraintsaints: 10110 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2153 5 %RANDOM
Rwork0.213 ---
all0.215 42928 --
obs-42928 98.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2648.48
Refinement stepCycle: LAST / Resolution: 1.87→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 8 191 2653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0238
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.192
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.084
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obs% reflection obs (%)
1.87-1.91X-RAY DIFFRACTION485386.5
1.91-1.96X-RAY DIFFRACTION530294.5
1.96-2.01X-RAY DIFFRACTION562799.6
2.01-2.07X-RAY DIFFRACTION5654100

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