[English] 日本語
Yorodumi
- PDB-3upd: 2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3upd
Title2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha and beta proteins (a/b) / ATC-like / Aspartate/ornithine carbamoyltransferase
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
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)39,6421
Polymers39,6421
Non-polymers00
Water84747
1
A: Ornithine carbamoyltransferase

A: Ornithine carbamoyltransferase

A: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)118,9263
Polymers118,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area6510 Å2
ΔGint-15 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.963, 153.963, 153.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 39641.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: argF, VV1_1466 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q8DCF5, ornithine carbamoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7.2mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: Calssics II (C2), 1.1M Ammonium tartrate (pH 7.0); Cryo: 4.0M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 13533 / Num. obs: 13533 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 82.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.3 / Num. unique all: 642 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUV

1duv


Resolution: 2.91→28.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 23.258 / SU ML: 0.191
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19452 669 4.9 %RANDOM
Rwork0.15799 ---
all0.15978 12861 --
obs0.15978 12861 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.788 Å2
Refinement stepCycle: LAST / Resolution: 2.91→28.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 47 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222753
X-RAY DIFFRACTIONr_bond_other_d0.0010.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9383715
X-RAY DIFFRACTIONr_angle_other_deg0.88534479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8985344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.98125132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73115475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6371511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_mcbond_it0.8821.51709
X-RAY DIFFRACTIONr_mcbond_other0.1531.5711
X-RAY DIFFRACTIONr_mcangle_it1.73122728
X-RAY DIFFRACTIONr_scbond_it2.74731044
X-RAY DIFFRACTIONr_scangle_it4.3764.5987
LS refinement shellResolution: 2.905→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 54 -
Rwork0.264 917 -
obs-917 100 %
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)
14.888812.5791.957532.49485.962712.73420.3766-0.20650.82691.2944-0.44561.86380.67220.59380.06891.42720.2947-0.2260.9319-0.32021.388524.5251-0.323932.9364
20.87980.3111-0.1021.8405-0.39931.08140.01020.17870.0082-0.18980.03930.06260.024-0.1465-0.04950.04450.01370.00250.09870.00020.008221.0386-22.041630.7513
34.72951.0081-0.71790.88720.22833.1969-0.15220.6074-0.2804-0.51820.1581-0.13610.21110.0211-0.00590.4306-0.02830.06350.197-0.0440.025532.1102-18.03710.9466
41.0318-0.3516-0.30010.9763-0.39032.37510.03950.14920.0501-0.2206-0.1185-0.2249-0.06990.31450.0790.1266-0.02140.08740.09810.01070.071640.0707-13.825823.2839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-22 - -17
2X-RAY DIFFRACTION2A-5 - 183
3X-RAY DIFFRACTION3A184 - 249
4X-RAY DIFFRACTION4A250 - 334

+
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