[English] 日本語
Yorodumi
- PDB-2w37: CRYSTAL STRUCTURE OF THE HEXAMERIC CATABOLIC ORNITHINE TRANSCARBA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w37
TitleCRYSTAL STRUCTURE OF THE HEXAMERIC CATABOLIC ORNITHINE TRANSCARBAMYLASE FROM Lactobacillus hilgardii
ComponentsORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
KeywordsTRANSFERASE / TRANSCARBAMYLASE / METAL BINDING-SITE / HEXAMER / CYTOPLASM / ORNITHINE / ARGININE METABOLISM / CARBAMOYL PHOSPHATE
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine catabolic process to ornithine / amino acid binding / metal ion 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
NICKEL (II) ION / Ornithine carbamoyltransferase, catabolic
Similarity search - Component
Biological speciesLACTOBACILLUS HILGARDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde las Rivas, B. / Fox, G.C. / Angulo, I. / Rodriguez, H. / Munoz, R. / Mancheno, J.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the Hexameric Catabolic Ornithine Transcarbamylase from Lactobacillus Hilgardii: Structural Insights Into the Oligomeric Assembly and Metal Binding.
Authors: De Las Rivas, B. / Fox, G.C. / Angulo, I. / Ripoll, M.M. / Rodriguez, H. / Munoz, R. / Mancheno, J.M.
History
DepositionNov 6, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
B: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
C: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4584
Polymers120,4003
Non-polymers591
Water5,999333
1
A: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
B: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
C: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
hetero molecules

A: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
B: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
C: ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,9178
Polymers240,8006
Non-polymers1172
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y,x,-z-11
Buried area20890 Å2
ΔGint-83.12 kcal/mol
Surface area69420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.805, 156.805, 80.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 3 - 343 / Label seq-ID: 19 - 359

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

-
Components

#1: Protein ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC / ORNITHINE TRANSCARBAMYLASE / OTCASE


Mass: 40133.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS HILGARDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q8G998, ornithine carbamoyltransferase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.1→78 Å / Num. obs: 63810 / % possible obs: 95.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXH

1dxh


Resolution: 2.1→69.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.501 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3216 5 %RANDOM
Rwork0.196 ---
obs0.198 60594 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.67 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8031 0 1 333 8365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.95311052
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53651020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13925.118381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1411533
X-RAY DIFFRACTIONr_chiral_restr0.0980.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026162
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23969
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.25505
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2482
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.55217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18228133
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63833360
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5264.52919
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1364medium positional0.160.5
2B1364medium positional0.160.5
3C1364medium positional0.140.5
1A1313loose positional0.415
2B1313loose positional0.375
3C1313loose positional0.365
1A1364medium thermal0.82
2B1364medium thermal0.962
3C1364medium thermal0.892
1A1313loose thermal1.5310
2B1313loose thermal1.8110
3C1313loose thermal1.6710
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 162
Rwork0.267 3391

+
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://pdbjlc1.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