[English] 日本語
Yorodumi
- PDB-4pq1: Crystal structure and functional implications of a DsbF homologue... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pq1
TitleCrystal structure and functional implications of a DsbF homologue from Corynebacterium diphtheriae
ComponentsPutative electron transport related protein
KeywordsOXIDOREDUCTASE / Thioredoxin-like region / reductant / oxidant
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
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
Putative electron transport related protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsUm, S.H. / Kim, J.S. / Yoon, B.Y. / Ha, N.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of a DsbF homologue from Corynebacterium diphtheriae.
Authors: Um, S.H. / Kim, J.S. / Lee, K. / Ha, N.C.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative electron transport related protein
B: Putative electron transport related protein


Theoretical massNumber of molelcules
Total (without water)34,6152
Polymers34,6152
Non-polymers00
Water2,684149
1
A: Putative electron transport related protein


Theoretical massNumber of molelcules
Total (without water)17,3071
Polymers17,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative electron transport related protein


Theoretical massNumber of molelcules
Total (without water)17,3071
Polymers17,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.103, 36.162, 62.522
Angle α, β, γ (deg.)90.00, 67.89, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative electron transport related protein / DsbF


Mass: 17307.289 Da / Num. of mol.: 2 / Fragment: UNP residues 29-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: NCTC 13129 / Gene: DIP0411 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NJJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M tris-HCl, 30% PEG 4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.097→36.181 Å / Num. all: 19396 / Num. obs: 18081 / % possible obs: 93.22 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.65 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.09-2.2186
2.2-2.34188
2.34-2.5210.91
2.52-2.78193
2.78-3.18196
3.18-4199

-
Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.097→36.181 Å / FOM work R set: 0.8017 / SU ML: 0.27 / σ(F): 1.52 / σ(I): 0 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 914 5.05 %RANDOM
Rwork0.1836 ---
obs0.1868 17168 93.22 %-
all-19396 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.53 Å2 / Biso mean: 34.04 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: LAST / Resolution: 2.097→36.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 0 149 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082515
X-RAY DIFFRACTIONf_angle_d1.0883426
X-RAY DIFFRACTIONf_chiral_restr0.042383
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d14.193916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0967-2.20720.34121130.28272238235186
2.2072-2.34540.30461090.26622310241988
2.3454-2.52650.30691480.23012341248991
2.5265-2.78070.28281320.21762454258693
2.7807-3.18280.23591440.18522487263196
3.1828-4.00920.23061250.15992647277299
4.0092-36.18620.20651430.13852691283499

+
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