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- PDB-1dxh: Catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1dxh
TitleCatabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa
ComponentsORNITHINE CARBAMOYLTRANSFERASEOrnithine transcarbamylase
KeywordsTRANSFERASE / TRANSCARBAMYLASE
Function / homology
Function and homology information


arginine deiminase pathway / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / arginine catabolic process to ornithine / 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, catabolic
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSainz, G. / Vicat, J. / Kahn, R. / Duee, E. / Tricot, C. / Stalon, V. / Dideberg, O.
Citation
Journal: To be Published
Title: Crystal Structure of the Allosteric Active Form of Catabolic Ornithine Carbamoyltransferase from Pseudomonas Aeruginosa
Authors: Sainz, G. / Vicat, J. / Kahn, R. / Duee, E. / Tricot, C. / Stalon, V. / Dideberg, O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, Crystallization and Preliminary X-Ray Analysis of Catabolic Ornithine Carbamoyltransferase from Pseudomonas Aeruginosa
Authors: Sainz, G. / Vicat, J. / Kahn, R. / Tricot, C. / Stalon, V. / Dideberg, O.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Allosteric Regulation in Pseudomonas Aeruginosa Catabolic Ornithine Carbamoyltransferase Revisited : Association of Concerted Homotropic Cooperative Interactions and Local Heterotropic Effects
Authors: Tricot, C. / Villeret, V. / Sainz, G. / Dideberg, O. / Stalon, V.
#3: Journal: Eur.J.Biochem. / Year: 1998
Title: Kinetic Studies of Allosteric Catabolic Ornithine Carbamoyltransferase from Pseudomonas Aeruginosa
Authors: Sainz, G. / Tricot, C. / Foray, M.F. / Marion, D. / Dideberg, O. / Stalon, V.
History
DepositionJan 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 6, 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)38,3184
Polymers38,0301
Non-polymers2883
Water1,874104
1
A: ORNITHINE CARBAMOYLTRANSFERASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)459,82248
Polymers456,36412
Non-polymers3,45836
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation6_566z,-x+1,-y+11
Buried area55980 Å2
ΔGint-404.56 kcal/mol
Surface area127810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.320, 134.320, 134.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-338-

SO4

21A-338-

SO4

31A-339-

SO4

41A-339-

SO4

51A-2026-

HOH

61A-2027-

HOH

71A-2103-

HOH

DetailsBIOLOGICAL_UNIT: DODECAMERTHE ASYMMETRIC UNIT CONTAINS 3 SULPHATE IONS.THE FIRST, SO4 340, IS ORDERED, WHILE THE OTHERS AREDISORDERED AND LIE ON THE THREE-FOLD AXIS RELATING(X,Y,Z) ,(1-Z , X, 1-Y) AND (Y, 1-Z, 1-X) AND AREREPRESENTED BY THE SO4 RESIDUES 338 AND 339. THREE WATER MOLECULES ARE ALSO ON THE THREE-FOLD AXIS,601,603 AND 624. THE LAST ONE IS ASSOCIATED WITH THESO4 RESIDUE 339

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Components

#1: Protein ORNITHINE CARBAMOYLTRANSFERASE / Ornithine transcarbamylase / ORNITHINE TRANSCARBAMYLASE


Mass: 38030.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P08308, ornithine carbamoyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.64 Å3/Da / Density % sol: 53.67 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal
*PLUS
Density % sol: 47.5 %
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.85 Mammonium sulfate1reservoir
350 mMHEPES1reservoirpH7.2
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir
62 %PEG4001reservoir
710 mMspermidine1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: BRUKER NONIUS / Detector: AREA DETECTOR
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 13231 / % possible obs: 95.4 % / Redundancy: 5.58 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.075
Reflection shellResolution: 2.5→2.61 Å / Rsym value: 0.252 / % possible all: 67.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. measured all: 80597 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 65.5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MADNESSdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ORT

1ort


Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 676 5 %RANDOM
Rwork0.179 ---
obs0.179 13231 95.4 %-
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 11 104 2784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2948 46 4.2 %
Rwork0.2489 1104 -
obs--67.25 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19X.PRO

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