[English] 日本語
Yorodumi
- PDB-6e8l: Crystal Structure of Alkyl hydroperoxidase D (AhpD) from Streptoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e8l
TitleCrystal Structure of Alkyl hydroperoxidase D (AhpD) from Streptococcus pneumoniae (Strain D39/ NCTC 7466)
ComponentsAlkyl hydroperoxide reductase AhpD
KeywordsOXIDOREDUCTASE / alkylhydroperoxidase peroxiredoxin
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / AhpD-like / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CMD domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMeng, Y. / Davies, J. / North, R. / Coombes, D. / Horne, C. / Hampton, M. / Dobson, R.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure-function analyses of alkylhydroperoxidase D fromStreptococcus pneumoniaereveal an unusual three-cysteine active site architecture.
Authors: Meng, Y. / Sheen, C.R. / Magon, N.J. / Hampton, M.B. / Dobson, R.C.J.
History
DepositionJul 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD
C: Alkyl hydroperoxide reductase AhpD
D: Alkyl hydroperoxide reductase AhpD
E: Alkyl hydroperoxide reductase AhpD
F: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)119,1206
Polymers119,1206
Non-polymers00
Water4,071226
1
A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)39,7072
Polymers39,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-31 kcal/mol
Surface area15190 Å2
MethodPISA
2
C: Alkyl hydroperoxide reductase AhpD
E: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)39,7072
Polymers39,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-31 kcal/mol
Surface area15370 Å2
MethodPISA
3
D: Alkyl hydroperoxide reductase AhpD
F: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)39,7072
Polymers39,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-32 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.296, 84.233, 183.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Alkyl hydroperoxide reductase AhpD


Mass: 19853.406 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: SPD_0373 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2ZNM1, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.123806 Å3/Da / Density % sol: 42.12108 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris propane, 0.2 M Magnesium chloride hexahydrate, 25% w/v PEG 3350, 6% v/v 1,2-Propandiol

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953717 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953717 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 45900 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.044 / Rrim(I) all: 0.106 / Χ2: 1 / Net I/σ(I): 10.5
Reflection shellResolution: 2.44→2.54 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4142 / CC1/2: 0.859 / Rpim(I) all: 0.212 / Rrim(I) all: 0.518 / Χ2: 0.91 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
Coot0.8.7model building
PHENIXrefinement
RefinementResolution: 2.3→45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.242 --
Rwork0.196 --
obs-45900 99.3 %
Refinement stepCycle: LAST / Resolution: 2.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8287 0 0 226 8513

+
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