[English] 日本語
Yorodumi
- PDB-3ot1: Crystal structure of VC2308 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ot1
TitleCrystal structure of VC2308 protein
Components(4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme) x 2
KeywordsSTRUCTURAL GENOMICS / CSGID / Vibrio cholerae / Center for Structural Genomics of Infectious Diseases / DJ-1 superfamily / UNKNOWN FUNCTION
Function / homology
Function and homology information


protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / protein deglycase activity / thiamine biosynthetic process / catalytic activity / cytosol
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å
AuthorsNiedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. ...Niedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of VC2308 protein
Authors: Niedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural ...Authors: Niedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme
B: 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8215
Polymers44,7272
Non-polymers943
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-49 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.387, 64.683, 81.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme


Mass: 22355.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS at residue 108
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC2308, VC_2308 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q9KPQ8
#2: Protein 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme


Mass: 22371.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSX at residue 108
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC2308, VC_2308 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q9KPQ8
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 1.9 Å3/Da / Density % sol: 35.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tacsimate 35%, Phenol 10mM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2010 / Details: beryllium lenses
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. all: 115862 / Num. obs: 115862 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.12 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 23.8
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4962 / Rsym value: 0.61 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
MD2data collection
HKL-3000MLPHAREphasing
DMmodel building
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.16→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.981 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.037
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16775 5797 5 %RANDOM
Rwork0.14357 ---
all0.1448 109812 --
obs0.1448 109812 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.231 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 3 579 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223236
X-RAY DIFFRACTIONr_bond_other_d0.0020.022120
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9644447
X-RAY DIFFRACTIONr_angle_other_deg2.33435245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69724.427131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9815536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7881517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213736
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02643
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2971.52100
X-RAY DIFFRACTIONr_mcbond_other1.5431.5850
X-RAY DIFFRACTIONr_mcangle_it1.93223390
X-RAY DIFFRACTIONr_scbond_it2.92631136
X-RAY DIFFRACTIONr_scangle_it4.2364.51032
X-RAY DIFFRACTIONr_rigid_bond_restr1.37333236
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 359 -
Rwork0.253 7215 -
obs--87.37 %

+
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