[English] 日本語
Yorodumi
- PDB-8ejn: Structure of dehaloperoxidase A in complex with 2,4-dichlorophenol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ejn
TitleStructure of dehaloperoxidase A in complex with 2,4-dichlorophenol
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidase / peroxygenase / oxydation / substrate / heme / cofactor / oxygen binding
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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,4-dichlorophenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.481 Å
AuthorsAktar, M.S. / de Serrano, V.S. / Franzen, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B.
Authors: Aktar, M.S. / de Serrano, V. / Ghiladi, R. / Franzen, S.
History
DepositionSep 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Derived calculations / Structure summary
Category: pdbx_entry_details / struct_conn / struct_conn_type
Item: _pdbx_entry_details.nonpolymer_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,28113
Polymers31,0972
Non-polymers2,18411
Water5,747319
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5165
Polymers15,5491
Non-polymers9684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7658
Polymers15,5491
Non-polymers1,2167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.881, 67.323, 69.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dehaloperoxidase A


Mass: 15548.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NAV8

-
Non-polymers , 6 types, 330 molecules

#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-5JC / 2,4-dichlorophenol


Mass: 163.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4Cl2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Nonpolymer detailsIn chain A internal conformation of H55 (conformation A) is not possible when the substrate is ...In chain A internal conformation of H55 (conformation A) is not possible when the substrate is bound. When the substrate (5JC) is bound His55 is oriented such that it is facing outside of the heme pocket, and it cannot be present inside because the substrate is bound close to the area where Hiss55 would be otherwise located.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 27-33% PEG 4000, 0.2 M Ammonium Sulfate, 0.020 M Sodium Cacodylate, pH 6.0-6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→37.091 Å / Num. obs: 44772 / % possible obs: 98.03 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Net I/σ(I): 21.9
Reflection shellResolution: 1.481→1.519 Å / Rmerge(I) obs: 0.641 / Num. unique obs: 3047 / CC1/2: 0.701 / Rpim(I) all: 0.369

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EW6

1ew6


Resolution: 1.481→37.091 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.812 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2111 2306 5.151 %
Rwork0.1597 42466 -
all0.162 --
obs-44772 98.029 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.254 Å2
Baniso -1Baniso -2Baniso -3
1--2.601 Å2-0 Å20 Å2
2--2.087 Å2-0 Å2
3---0.513 Å2
Refinement stepCycle: LAST / Resolution: 1.481→37.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 140 319 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152288
X-RAY DIFFRACTIONr_angle_refined_deg1.881.7053421
X-RAY DIFFRACTIONr_angle_other_deg1.631.6255259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00922.273132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04215429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9691516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022940
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02644
X-RAY DIFFRACTIONr_nbd_refined0.2430.2687
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22130
X-RAY DIFFRACTIONr_nbtor_refined0.180.21222
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2228
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.232
X-RAY DIFFRACTIONr_nbd_other0.2150.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.228
X-RAY DIFFRACTIONr_mcbond_it1.6361.0651171
X-RAY DIFFRACTIONr_mcbond_other1.6371.0651170
X-RAY DIFFRACTIONr_mcangle_it1.9771.6181483
X-RAY DIFFRACTIONr_mcangle_other1.9761.6181484
X-RAY DIFFRACTIONr_scbond_it3.3661.4091346
X-RAY DIFFRACTIONr_scbond_other3.3721.4131339
X-RAY DIFFRACTIONr_scangle_it3.8371.971938
X-RAY DIFFRACTIONr_scangle_other3.8421.9731927
X-RAY DIFFRACTIONr_lrange_it4.49214.8053246
X-RAY DIFFRACTIONr_lrange_other4.27314.2363174
X-RAY DIFFRACTIONr_rigid_bond_restr9.30234805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.481-1.5190.3691590.3253047X-RAY DIFFRACTION97.0045
1.519-1.5610.2261740.2183091X-RAY DIFFRACTION99.6947
1.561-1.6060.2281640.1842991X-RAY DIFFRACTION99.684
1.606-1.6560.2181450.1632906X-RAY DIFFRACTION99.6082
1.656-1.710.2221690.1522779X-RAY DIFFRACTION99.4602
1.71-1.770.1861300.1432731X-RAY DIFFRACTION99.3748
1.77-1.8370.21490.1422601X-RAY DIFFRACTION99.1706
1.837-1.9110.231450.1592511X-RAY DIFFRACTION98.4068
1.911-1.9960.2331430.1572380X-RAY DIFFRACTION97.8666
1.996-2.0940.2141270.1492325X-RAY DIFFRACTION98.316
2.094-2.2070.1751250.1422177X-RAY DIFFRACTION98.4602
2.207-2.340.2291010.1472044X-RAY DIFFRACTION95.8874
2.34-2.5010.161140.1271959X-RAY DIFFRACTION97.9216
2.501-2.7010.1861020.1361817X-RAY DIFFRACTION97.8084
2.701-2.9580.191910.1391678X-RAY DIFFRACTION97.0911
2.958-3.3060.206580.1561544X-RAY DIFFRACTION96.6807
3.306-3.8140.213870.1511310X-RAY DIFFRACTION95.2284
3.814-4.6640.166500.1481154X-RAY DIFFRACTION95.3286
4.664-6.5650.243480.215892X-RAY DIFFRACTION93.7188
6.565-37.0910.342250.216529X-RAY DIFFRACTION91.1184

+
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