[English] 日本語
Yorodumi
- PDB-5k8z: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k8z
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 (pH 8.5)
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold
Function / homology
Function and homology information


oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #3420 / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROXIDE ION / Chlorite dismutase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPuehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins, BioToP) Austria
Austrian Science FundFWF P25270 Austria
Austrian Science FundFWF P22276 Austria
CitationJournal: ACS Catal / Year: 2017
Title: Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies.
Authors: Schaffner, I. / Mlynek, G. / Flego, N. / Puhringer, D. / Libiseller-Egger, J. / Coates, L. / Hofbauer, S. / Bellei, M. / Furtmuller, P.G. / Battistuzzi, G. / Smulevich, G. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chlorite dismutase
B: Chlorite dismutase
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,33016
Polymers87,3244
Non-polymers3,00712
Water14,232790
1
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1658
Polymers43,6622
Non-polymers1,5036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1658
Polymers43,6622
Non-polymers1,5036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.858, 72.833, 112.494
Angle α, β, γ (deg.)90.000, 94.570, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Chlorite dismutase /


Mass: 21830.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria)
Gene: Cyan7425_1434 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B8HNS6

-
Non-polymers , 5 types, 802 molecules

#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% (w/v) PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2015 / Details: KB-mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.55→44.428 Å / Num. obs: 127776 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1482 / Net I/σ(I): 6.24
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 0.89 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_2712refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
EDNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QPI

3qpi


Resolution: 1.55→44.428 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1311 1.03 %
Rwork0.1981 126337 -
obs0.1984 127648 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.73 Å2 / Biso mean: 29.4213 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 1.55→44.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5968 0 388 790 7146
Biso mean--22.23 30.9 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056385
X-RAY DIFFRACTIONf_angle_d0.7268713
X-RAY DIFFRACTIONf_chiral_restr0.047889
X-RAY DIFFRACTIONf_plane_restr0.0041110
X-RAY DIFFRACTIONf_dihedral_angle_d12.1363711
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5498-1.61190.36131370.34311400714144100
1.6119-1.68530.3191500.31081398914139100
1.6853-1.77410.29261470.29231394714094100
1.7741-1.88530.2991460.2551399414140100
1.8853-2.03080.25391460.21311404814194100
2.0308-2.23520.2111490.18881399814147100
2.2352-2.55860.22231440.17921405914203100
2.5586-3.22340.20591420.17511411214254100
3.2234-44.44660.18431500.1517141831433399

+
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