[English] 日本語
Yorodumi
- PDB-3ey7: Structure from the mobile metagenome of V. Cholerae. Integron cas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ey7
TitleStructure from the mobile metagenome of V. Cholerae. Integron cassette protein VCH_CASS1
ComponentsBiphenyl-2,3-diol 1,2-dioxygenase III-related protein
KeywordsOXIDOREDUCTASE / Integron Cassette protein mobile metagenome Structural Genomics / Dioxygenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHarrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. ...Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure from the mobile metagenome of V. Cholerae. Integron cassette protein VCH_CASS1
Authors: Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
B: Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7924
Polymers29,7122
Non-polymers802
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-52 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.029, 67.868, 91.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Biphenyl-2,3-diol 1,2-dioxygenase III-related protein


Mass: 14856.071 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0328, VC_A0341, VC_A0463 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q9K3D3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 9% PEG 8000, 0.2M Ca(OAC), 0.1M NA Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→54.47 Å / Num. obs: 34682 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 15.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4882 / Rsym value: 0.43 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→27.754 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 2000 5.77 %RANDOM
Rwork0.1712 ---
obs0.1738 34641 96.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.252 Å2 / ksol: 0.32 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→27.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 2 432 2515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.27171370.22372236X-RAY DIFFRACTION95
1.64-1.68440.2641380.20982242X-RAY DIFFRACTION95
1.6844-1.73390.24561400.19712289X-RAY DIFFRACTION95
1.7339-1.78990.23851400.18772293X-RAY DIFFRACTION96
1.7899-1.85380.23531410.17982289X-RAY DIFFRACTION96
1.8538-1.92810.25761420.1822330X-RAY DIFFRACTION96
1.9281-2.01580.24241400.17932284X-RAY DIFFRACTION96
2.0158-2.1220.21291430.1752336X-RAY DIFFRACTION97
2.122-2.25490.18751430.16932338X-RAY DIFFRACTION97
2.2549-2.42890.2151450.17292358X-RAY DIFFRACTION97
2.4289-2.67320.21461450.17212371X-RAY DIFFRACTION98
2.6732-3.05960.22431470.17122390X-RAY DIFFRACTION98
3.0596-3.85310.20851480.14852424X-RAY DIFFRACTION98
3.8531-27.75820.18151510.14912461X-RAY DIFFRACTION95

+
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://pdbjlvh1.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