[English] 日本語
Yorodumi
- PDB-1dxh: Catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


L-arginine deiminase pathway / 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, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein ORNITHINE CARBAMOYLTRANSFERASE / 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


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


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more