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- PDB-1a1s: ORNITHINE CARBAMOYLTRANSFERASE FROM PYROCOCCUS FURIOSUS -

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Basic information

Entry
Database: PDB / ID: 1a1s
TitleORNITHINE CARBAMOYLTRANSFERASE FROM PYROCOCCUS FURIOSUS
ComponentsORNITHINE CARBAMOYLTRANSFERASE
KeywordsTRANSCARBAMYLASE
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVilleret, V. / Clantin, B. / Tricot, C. / Legrain, C. / Roovers, M. / Stalon, V. / Glansdorff, N. / Van Beeumen, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures.
Authors: Villeret, V. / Clantin, B. / Tricot, C. / Legrain, C. / Roovers, M. / Stalon, V. / Glansdorff, N. / Van Beeumen, J.
History
DepositionDec 15, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORNITHINE CARBAMOYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)35,0981
Polymers35,0981
Non-polymers00
Water00
1
A: ORNITHINE CARBAMOYLTRANSFERASE
x 12


Theoretical massNumber of molelcules
Total (without water)421,17812
Polymers421,17812
Non-polymers00
Water0
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 area41430 Å2
ΔGint-182 kcal/mol
Surface area117470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)186.800, 186.800, 186.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein ORNITHINE CARBAMOYLTRANSFERASE / ORNITHINE TRANSCARBAMYLASE


Mass: 35098.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q51742, ornithine carbamoyltransferase

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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: 3.87 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 294 K / pH: 4
Details: THE PROTEIN WAS CRYSTALLIZED FROM 1M NACL, 100 MM ACETATE, PH 4.0, 21 DEGREES C, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / 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
112 mg/mlprotein1drop
21 M1reservoirNaCl
3100 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 14893 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 12.4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.85 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 3 / Rsym value: 0.288 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→10 Å / Rfactor Rfree error: 0.022 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.258 140 10 %RANDOM
Rwork0.226 ---
obs0.226 14853 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 0 0 2454
LS refinement shellResolution: 2.7→2.78 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.36 -
Rwork0.32 -
obs-99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.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_bond_d0.09
X-RAY DIFFRACTIONx_angle_deg1.7
LS refinement shell
*PLUS
Rfactor obs: 0.32

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