[English] 日本語
Yorodumi
- PDB-3gkn: Insights into the Alkyl Peroxide Reduction Activity of Xanthomona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gkn
TitleInsights into the Alkyl Peroxide Reduction Activity of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate/Ligand Complex Structures
ComponentsBacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / Xanthomonas campestris / Bcp / Prx / Atypical 2-Cys
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm
Similarity search - Function
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAPHTHALENE-2,6-DISULFONIC ACID / Peroxiredoxin Bcp
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLiao, S.-J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structures
Authors: Liao, S.-J. / Yang, C.-Y. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: 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 1.4Nov 1, 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: Bacterioferritin comigratory protein
B: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,78516
Polymers35,0802
Non-polymers1,70614
Water6,593366
1
A: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4819
Polymers17,5401
Non-polymers9418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3057
Polymers17,5401
Non-polymers7656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.110, 56.490, 74.900
Angle α, β, γ (deg.)90.00, 119.55, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17539.963 Da / Num. of mol.: 2 / Mutation: C48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: 17 / Gene: BCP / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8P9V9, peroxiredoxin
#2: Chemical ChemComp-BIH / NAPHTHALENE-2,6-DISULFONIC ACID / 2,6-NAPHTHALENEDISULFONIC ACID / 2,6-NAPHTHALENEDISULPHONIC ACID


Mass: 288.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O6S2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 53.62 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 1.7M (NH4)2SO4, 0.2M NaCl, 0.1M Na cacodylate pH 6.5, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 60047 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 25.58
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.16 / Rsym value: 0.426 / % possible all: 92.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GKK

3gkk


Resolution: 1.47→24.88 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2856 4.6 %RANDOM
Rwork0.198 ---
obs0.198 54389 91.5 %-
all-57245 --
Solvent computationBsol: 55.918 Å2
Displacement parametersBiso mean: 21.094 Å2
Baniso -1Baniso -2Baniso -3
1-2.128 Å20 Å2-1.005 Å2
2---0.524 Å20 Å2
3----1.604 Å2
Refinement stepCycle: LAST / Resolution: 1.47→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 102 366 2846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.238
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.47→1.52 Å / % reflection Rfree: 5 % / % reflection obs: 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3NDAD_GC_PAR.TXTNDAD_GC_TOP.TXT

+
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