[English] 日本語
Yorodumi
- PDB-3c71: Structure of a ResA variant with a DsbA-like active site motif (CPHC) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c71
TitleStructure of a ResA variant with a DsbA-like active site motif (CPHC)
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / Thioredoxin-like fold / Cytochrome c-type biogenesis / Membrane / Redox-active center / Signal-anchor / Transmembrane
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / antioxidant activity / plasma membrane
Similarity search - Function
Thiol-disulphide oxidoreductase ResA / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol-disulphide oxidoreductase ResA / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol-disulfide oxidoreductase ResA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCrow, A.
CitationJournal: Biochem.J. / Year: 2008
Title: Effects of substitutions in the CXXC active-site motif of the extracytoplasmic thioredoxin ResA.
Authors: Lewin, A. / Crow, A. / Hodson, C.T. / Hederstedt, L. / Le Brun, N.E.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 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 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiol-disulfide oxidoreductase resA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0132
Polymers15,9511
Non-polymers621
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.975, 36.975, 177.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Thiol-disulfide oxidoreductase resA


Mass: 15951.164 Da / Num. of mol.: 1 / Fragment: UNP residues 37-179 / Mutation: E75P, P76H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: resA, ypxA / Production host: Escherichia coli (E. coli) / References: UniProt: P35160
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 27% PEG 4000, 0.1M tri-Sodium Citrate pH 5.6, 0.2 M Ammonium acetate, 10mM DTT. Protein concentration was 15 mg/ml, in 20 mM MOPS pH 7., VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ESRF / Detector: CCD / Date: Feb 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→32.03 Å / Num. all: 10145 / Num. obs: 10145 / % possible obs: 93.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rsym value: 0.087 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 1071 / Rsym value: 0.125 / % possible all: 67.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→21.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.541 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Author states that the bad geometry of PRO A139 is caused by the fact that the preceding residue has an alternative conformation.
RfactorNum. reflection% reflectionSelection details
Rfree0.21112 471 4.7 %RANDOM 5%
Rwork0.16416 ---
obs0.16651 9612 93.34 %-
all-10145 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 4 123 1228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221206
X-RAY DIFFRACTIONr_angle_refined_deg2.3641.9531643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9095154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06625.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78615210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.451153
X-RAY DIFFRACTIONr_chiral_restr0.1290.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02927
X-RAY DIFFRACTIONr_nbd_refined0.2030.2577
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.214
X-RAY DIFFRACTIONr_mcbond_it0.8771.5766
X-RAY DIFFRACTIONr_mcangle_it1.35621221
X-RAY DIFFRACTIONr_scbond_it2.2123501
X-RAY DIFFRACTIONr_scangle_it3.5774.5422
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 18 -
Rwork0.187 451 -
obs--55.83 %

+
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