[English] 日本語
Yorodumi
- PDB-8vqu: Crystal Structure of Dehaloperoxidase B in complex with substrate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vqu
TitleCrystal Structure of Dehaloperoxidase B in complex with substrate 1,4-cyclohexadiene
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / peroxidase / peroxigenase / oxidase / oxygenase / globin / heme cofactor / oxygen binding / hydrogen peroxide co-substrate halophenol binding / substrates
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 / OXYGEN MOLECULE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
Authorsde Seerano, V.S. / Yun, D. / Ghiladi, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Crystal Structure of Dehaloperoxidase B in complex with substrate 1,4-cyclohexadiene
Authors: de Seerano, V.S. / Yun, D. / Ghiladi, R.A.
History
DepositionJan 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

-
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)32,92714
Polymers30,8292
Non-polymers2,09812
Water3,261181
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,76810
Polymers15,4141
Non-polymers1,3539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1594
Polymers15,4141
Non-polymers7453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.344, 66.704, 68.119
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 B


Mass: 15414.462 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: Q9NAV7

-
Non-polymers , 6 types, 193 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1ADJ / cyclohexa-1,4-diene


Mass: 80.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulfate, sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→17.77 Å / Num. obs: 26890 / % possible obs: 96.55 % / Redundancy: 5.3 % / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 1.751→1.796 Å / Num. unique obs: 1340 / CC1/2: 0.635

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→17.77 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.17 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2204 1345 5.002 %
Rwork0.1851 25545 -
all0.187 --
obs-26890 96.549 %
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: 23.268 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---0.152 Å20 Å2
3----1.308 Å2
Refinement stepCycle: LAST / Resolution: 1.751→17.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 138 181 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132784
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152538
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.7033831
X-RAY DIFFRACTIONr_angle_other_deg1.4331.6315896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02422.961152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9251518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023417
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02717
X-RAY DIFFRACTIONr_nbd_refined0.2490.2786
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22314
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21323
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2197
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.225
X-RAY DIFFRACTIONr_nbd_other0.2150.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_mcbond_it1.9562.2271309
X-RAY DIFFRACTIONr_mcbond_other1.9492.2251308
X-RAY DIFFRACTIONr_mcangle_it2.8643.341695
X-RAY DIFFRACTIONr_mcangle_other2.8653.3421696
X-RAY DIFFRACTIONr_scbond_it2.5982.5831475
X-RAY DIFFRACTIONr_scbond_other2.5622.5651452
X-RAY DIFFRACTIONr_scangle_it4.0393.7632116
X-RAY DIFFRACTIONr_scangle_other4.0293.7392086
X-RAY DIFFRACTIONr_lrange_it5.71227.913544
X-RAY DIFFRACTIONr_lrange_other5.65127.6933503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-1.7960.295770.2791340X-RAY DIFFRACTION70.85
1.796-1.8460.315790.2421643X-RAY DIFFRACTION87.2783
1.846-1.8990.3930.2321758X-RAY DIFFRACTION95.9067
1.899-1.9570.277890.2191756X-RAY DIFFRACTION99.5146
1.957-2.0210.2381170.2071700X-RAY DIFFRACTION100
2.021-2.0920.274810.1951679X-RAY DIFFRACTION100
2.092-2.1710.239950.1891615X-RAY DIFFRACTION100
2.171-2.260.214770.1671545X-RAY DIFFRACTION100
2.26-2.360.243610.1751513X-RAY DIFFRACTION100
2.36-2.4750.205920.1641423X-RAY DIFFRACTION100
2.475-2.6080.202640.1671366X-RAY DIFFRACTION100
2.608-2.7660.23650.1751296X-RAY DIFFRACTION100
2.766-2.9560.218730.1661222X-RAY DIFFRACTION100
2.956-3.1920.218430.191161X-RAY DIFFRACTION100
3.192-3.4950.203670.1821045X-RAY DIFFRACTION100
3.495-3.9050.229410.168977X-RAY DIFFRACTION100
3.905-4.5040.158500.155852X-RAY DIFFRACTION100
4.504-5.5040.18400.18730X-RAY DIFFRACTION100
5.504-7.7320.314260.212594X-RAY DIFFRACTION100
7.732-17.770.143150.143330X-RAY DIFFRACTION89.8438

+
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