[English] 日本語
Yorodumi
- PDB-4oh7: Crystal structure of Ornithine carbamoyltransferase from Brucella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oh7
TitleCrystal structure of Ornithine carbamoyltransferase from Brucella melitensis
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / SSGCID / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / 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
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Ornithine carbamoyltransferase from Brucella melitensis
Authors: Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9458
Polymers70,6262
Non-polymers3196
Water12,809711
1
A: Ornithine carbamoyltransferase
hetero molecules

A: Ornithine carbamoyltransferase
hetero molecules

A: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,41812
Polymers105,9393
Non-polymers4799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area7620 Å2
ΔGint-34 kcal/mol
Surface area31170 Å2
MethodPISA
2
B: Ornithine carbamoyltransferase
hetero molecules

B: Ornithine carbamoyltransferase
hetero molecules

B: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,41812
Polymers105,9393
Non-polymers4799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-y+1,x-y+3,z1
crystal symmetry operation3_365-x+y-2,-x+1,z1
Buried area7680 Å2
ΔGint-33 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.450, 88.450, 142.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-798-

HOH

21B-665-

HOH

-
Components

#1: Protein Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase / Ornithine carbamoyltransferase / catabolic


Mass: 35313.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: biotype 2 (strain ATCC 23457) / Gene: arcB, argF, BMEA_A0337 / Plasmid: BrmeB.00183.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0RH19, ornithine carbamoyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, ...Details: BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 100819 / Num. obs: 100352 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 23.829 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.540.392.43208487387199.2
1.54-1.580.3223.54262527241199.9
1.58-1.630.2654.38260897003199.9
1.63-1.680.2255.192554168731100
1.68-1.730.1886.23248426664199.9
1.73-1.790.1517.852386663791100
1.79-1.860.11910.04232056207199.9
1.86-1.940.09712.44222715972199.9
1.94-2.020.07516.03212045719199.9
2.02-2.120.0619.65201415477199.8
2.12-2.240.0522.78187905141199.3
2.24-2.370.04625.29177864911199.4
2.37-2.540.04227.35166614622199.5
2.54-2.740.03729.92153794302199.2
2.74-30.03532.89141023943199.4
3-3.350.03135.56126213552198.7
3.35-3.870.02838.17110503130198.5
3.87-4.740.02640.1496922667199.2
4.74-6.710.02440.2676992076198.9
6.71-500.02339.9238411086192.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL IN DIFFERENT SPACE GROUP OBTAINED FROM IODIDE PHASING

Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1797 / WRfactor Rwork: 0.1519 / FOM work R set: 0.8895 / SU B: 2.42 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0642 / SU Rfree: 0.0666 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 4848 4.8 %RANDOM
Rwork0.1546 ---
all0.1559 100819 --
obs0.1559 100315 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.76 Å2 / Biso mean: 19.044 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 18 711 5285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194843
X-RAY DIFFRACTIONr_bond_other_d0.0010.024669
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9556604
X-RAY DIFFRACTIONr_angle_other_deg0.859310758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10123.971204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07215831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5531533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025554
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021069
X-RAY DIFFRACTIONr_mcbond_it0.8691.0952475
X-RAY DIFFRACTIONr_mcbond_other0.8561.0942474
X-RAY DIFFRACTIONr_mcangle_it1.4091.6383108
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 307 -
Rwork0.222 7073 -
all-7380 -
obs-7073 99.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1885-0.602-0.14720.75960.08410.3817-0.0291-0.02950.03950.0761-0.0098-0.0442-0.05680.00810.03890.07770.0029-0.02810.048-0.00330.0127-51.92299.09715.717
21.1568-0.0414-0.0990.4373-0.1820.5678-0.02430.08330.0529-0.0044-0.0051-0.0692-0.06180.08020.02940.0382-0.0185-0.00690.0510.00020.0153-66.975112.117-18.723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 307
2X-RAY DIFFRACTION2B6 - 307

+
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