[English] 日本語
Yorodumi
- PDB-7adf: SFX structure of dehaloperoxidase B in the ferric form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7adf
TitleSFX structure of dehaloperoxidase B in the ferric form
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / SFX / ferric / dehaloperoxidase / peroxidase / fixed-target
Function / homology
Function and homology information


oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMoreno Chicano, T. / Ebrahim, A. / Axford, D.A. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Worrall, J.W. / Strange, R.W. / Owen, R.L. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: to be published
Title: SFX structure of dehaloperoxidase B in the ferric form
Authors: Moreno Chicano, T. / Carey, L.M. / Ebrahim, A. / Axford, D.A. / Beale, J.H. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Worrall, J.W. / Strange, R.W. / Owen, R.L. / Hough, M.A.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 15, 2025Group: Database references / Structure summary
Category: audit_author / citation_author / pdbx_entry_details
Item: _audit_author.name / _citation_author.name / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5166
Polymers31,0912
Non-polymers1,4254
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-57 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 67.910, 68.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Dehaloperoxidase B


Mass: 15545.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NAV7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: Microcrystals
Crystal growTemperature: 278 K / Method: batch mode / pH: 6
Details: Batch microcrystallization was used, mixing 30 mg/ml DHP in 20 mM MES pH 6.0 with 40%(w/v) PEG 4000, 200 mM ammonium sulfate in a 1 to 4 ratio in a total volume of 250 to 500 microlitres.

-
Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.85→37.9 Å / Num. obs: 25114 / % possible obs: 100 % / Redundancy: 486 % / CC1/2: 1 / R split: 0.078 / Net I/σ(I): 10.7
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 305 % / Num. unique obs: 1226 / CC1/2: 0.67 / R split: 0.603 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.675 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Silicon fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Oxford Chip / Sample dehydration prevention: Mylar film

-
Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3ixf

3ixf


Resolution: 1.85→33.955 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1221 4.87 %
Rwork0.1783 23834 -
obs0.18 25055 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.51 Å2 / Biso mean: 40.0014 Å2 / Biso min: 23.81 Å2
Refinement stepCycle: final / Resolution: 1.85→33.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 91 84 2281
Biso mean--46.62 43.34 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.85-1.92410.5211230.46952612
1.9241-2.01160.24811180.23652615
2.0116-2.11770.22931290.18222617
2.1177-2.25030.2381370.17672613
2.2503-2.4240.22591520.17872609
2.424-2.66790.22771180.17912655
2.6679-3.05370.22991600.18242638
3.0537-3.84650.17991170.1652699
3.8465-33.9550.19711670.16612776

+
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