[English] 日本語
Yorodumi
- PDB-1vlv: Crystal structure of Ornithine carbamoyltransferase (TM1097) from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vlv
TitleCrystal structure of Ornithine carbamoyltransferase (TM1097) from Thermotoga maritima at 2.25 A resolution
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / TM1097 / ORNITHINE CARBAMOYLTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via 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
PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ornithine carbamoyltransferase (TM1097) from Thermotoga maritima at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1554
Polymers36,8701
Non-polymers2853
Water1,69394
1
A: Ornithine carbamoyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)445,86448
Polymers442,44512
Non-polymers3,41936
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation28_565x,-y+3/2,-z+1/21
crystal symmetry operation31_664-z+1,-x+3/2,y-1/21
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation51_655-x+3/2,y,-z+1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation60_664-y+3/2,-z+1,x-1/21
crystal symmetry operation74_665-x+3/2,-y+3/2,z1
crystal symmetry operation78_566z+1/2,-x+3/2,-y+11
crystal symmetry operation82_656-y+3/2,z+1/2,-x+11
Buried area60820 Å2
ΔGint-323 kcal/mol
Surface area105440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)210.339, 210.339, 210.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-315-

PO4

21A-315-

PO4

31A-316-

PO4

41A-316-

PO4

51A-394-

HOH

-
Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 36870.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: argF / Production host: Escherichia coli (E. coli) / References: UniProt: P96108, ornithine carbamoyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.75 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.1
Details: 0.2% MPD, 0.2M NH4OAc, 0.1M Na,K-Phosphate pH 6.1, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Sep 20, 2003
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: 2.25→63.32 Å / Num. obs: 19349 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.84 Å2 / Rsym value: 0.071 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5014 / Num. unique all: 1366 / Rsym value: 0.734 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a1s

1a1s


Resolution: 2.25→63.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.355 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1), HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2), THE DENSITY BETWEEN 235-244 IS WEAK AND IT IS NOT POSSIBLE TO BUILD THE MISSING RESIDUES INTO IT. 3), TWO PO4 ANIONS ARE LOCATED AT ...Details: 1), HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2), THE DENSITY BETWEEN 235-244 IS WEAK AND IT IS NOT POSSIBLE TO BUILD THE MISSING RESIDUES INTO IT. 3), TWO PO4 ANIONS ARE LOCATED AT THE THREE-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS AT THE INTERFACE BETWEEN THREE MONOMERS. THE P AND O ATOMS ON THESE RESIDUES WERE MODELED WITH OCCUPANCIES OF 0.33.
RfactorNum. reflection% reflectionSelection details
Rfree0.21528 986 5.1 %RANDOM
Rwork0.18917 ---
obs0.19049 18186 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.765 Å2
Refinement stepCycle: LAST / Resolution: 2.25→63.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 15 94 2513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222458
X-RAY DIFFRACTIONr_bond_other_d0.0010.022249
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9633317
X-RAY DIFFRACTIONr_angle_other_deg0.88235210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1185306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40723.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65515439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3211518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2140.2473
X-RAY DIFFRACTIONr_nbd_other0.1820.22202
X-RAY DIFFRACTIONr_nbtor_other0.0870.21428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.214
X-RAY DIFFRACTIONr_mcbond_it0.7311.51571
X-RAY DIFFRACTIONr_mcbond_other0.1541.5628
X-RAY DIFFRACTIONr_mcangle_it1.14922457
X-RAY DIFFRACTIONr_scbond_it1.8233988
X-RAY DIFFRACTIONr_scangle_it2.7354.5860
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21154
LS refinement shellResolution: 2.25→2.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 65 4.85 %
Rwork0.293 1276 -
obs--96.41 %
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)
12.47650.5205-0.47992.07630.37591.9867-0.0324-0.1881-0.23720.21590.0013-0.30390.11820.24280.0311-0.24650.0125-0.0413-0.07870.0037-0.1561186.4236152.698865.1229
27.9252-7.0483-3.974612.03118.22715.81410.1606-0.27630.2241-0.2748-0.0036-0.1908-0.57690.2854-0.157-0.1828-0.063-0.0532-0.0323-0.0123-0.1812186.9914164.675775.5007
34.90310.2720.29192.4983-0.58714.26590.1088-0.38260.19370.2639-0.2066-0.4037-0.38161.08140.0979-0.1676-0.1617-0.14710.2923-0.05540.0251199.5501166.347680.6084
48.17731.2670.28252.6751-0.07813.70470.1213-1.22860.00060.5323-0.1954-0.3469-0.05530.75550.0742-0.0196-0.061-0.15310.3476-0.0501-0.1729190.847162.521192.651
53.9967-0.4772-0.20321.51150.0788.2463-0.0268-0.2097-0.03710.1528-0.0438-0.14030.1436-0.17340.0706-0.2731-0.0444-0.0424-0.1946-0.0149-0.1802180.8309159.485871.0387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-4 - 1348 - 146
22135 - 149147 - 161
33150 - 234162 - 246
44245 - 292257 - 304
55293 - 313305 - 325

+
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