[English] 日本語
Yorodumi
- PDB-6vds: Crystal Structure of Dehaloperoxidase B in Complex with cofactor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vds
TitleCrystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-bromo-ortho-cresol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxidase / peroxygenase / 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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
FE(III) DEUTEROPORPHYRIN IX / 4-bromo-2-methylphenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / McGuire, A. / Malewschik, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
Authors: McGuire, A.H. / Petit, A.R. / Kang, J. / Malewschik, T. / de Serrano, V. / Carey, L.M. / Ghiladi, R.A.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Data collection / Category: pdbx_reflns_twin
Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)33,02016
Polymers30,8292
Non-polymers2,19214
Water1,36976
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6069
Polymers15,4141
Non-polymers1,1928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4147
Polymers15,4141
Non-polymers1,0006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.562, 67.491, 67.951
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 (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS / References: UniProt: Q9NAV7

-
Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-FDE / FE(III) DEUTEROPORPHYRIN IX


Mass: 564.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MWJ / 4-bromo-2-methylphenol


Mass: 187.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7BrO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium Sulphate MPEG 2000, 29-33%

-
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: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.6947
pseudo-merohedral11-H, L, K20.3053
ReflectionResolution: 1.97→47.89 Å / Num. obs: 19237 / % possible obs: 96.42 % / Redundancy: 9.1 % / CC1/2: 0.994 / Net I/σ(I): 22.3
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 930 / CC1/2: 0.646

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.97→47.885 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.46 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2558 1021 5.307 %
Rwork0.2154 --
all0.218 --
obs-19237 96.416 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.946 Å2
Baniso -1Baniso -2Baniso -3
1-6.818 Å20 Å20 Å2
2---1.33 Å2-0 Å2
3----5.488 Å2
Refinement stepCycle: LAST / Resolution: 1.97→47.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 138 76 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182421
X-RAY DIFFRACTIONr_angle_refined_deg2.3631.733790
X-RAY DIFFRACTIONr_angle_other_deg1.3351.635648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35522.329146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86615469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8951519
X-RAY DIFFRACTIONr_chiral_restr0.1640.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023320
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02650
X-RAY DIFFRACTIONr_nbd_refined0.220.2765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22165
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21257
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.222
X-RAY DIFFRACTIONr_nbd_other0.2110.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.214
X-RAY DIFFRACTIONr_mcbond_it1.2592.6531285
X-RAY DIFFRACTIONr_mcbond_other1.2582.6531284
X-RAY DIFFRACTIONr_mcangle_it1.8953.9731660
X-RAY DIFFRACTIONr_mcangle_other1.8943.9741661
X-RAY DIFFRACTIONr_scbond_it1.2912.9221464
X-RAY DIFFRACTIONr_scbond_other1.2742.9141457
X-RAY DIFFRACTIONr_scangle_it1.8494.3832112
X-RAY DIFFRACTIONr_scangle_other1.8364.372101
X-RAY DIFFRACTIONr_lrange_it4.38632.7323410
X-RAY DIFFRACTIONr_lrange_other4.34332.7193404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0220.305490.289930X-RAY DIFFRACTION68.2706
2.022-2.0770.489670.2681300X-RAY DIFFRACTION96.6761
2.077-2.1370.356630.2911290X-RAY DIFFRACTION97.9725
2.137-2.2030.307760.231241X-RAY DIFFRACTION97.5556
2.203-2.2750.208430.2581222X-RAY DIFFRACTION98.4436
2.275-2.3540.28830.251165X-RAY DIFFRACTION99.601
2.354-2.4430.325730.241114X-RAY DIFFRACTION97.0564
2.443-2.5420.229610.2251085X-RAY DIFFRACTION99.2208
2.542-2.6550.289460.2071055X-RAY DIFFRACTION97.8667
2.655-2.7840.278480.2271016X-RAY DIFFRACTION99.5323
2.784-2.9340.343750.215958X-RAY DIFFRACTION99.4225
2.934-3.1120.232310.233954X-RAY DIFFRACTION99.5956
3.112-3.3250.258460.219859X-RAY DIFFRACTION99.0153
3.325-3.590.28560.217812X-RAY DIFFRACTION100.6961
3.59-3.9310.228500.2719X-RAY DIFFRACTION96.3659
3.931-4.3910.199440.174676X-RAY DIFFRACTION99.5851
4.391-5.0630.219310.179623X-RAY DIFFRACTION99.2413
5.063-6.1840.182400.217517X-RAY DIFFRACTION100.1798
6.184-8.6740.187200.192429X-RAY DIFFRACTION100.2232
8.674-47.8850.254190.181251X-RAY DIFFRACTION98.1818
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0669-0.1609-0.08350.56630.03040.2706-0.01820.0009-0.00950.0683-0.0256-0.0143-0.00840.00920.04380.0203-0.0104-0.00170.0790.01440.01083.71441.8438-18.5194
20.5960.61210.60891.33650.37230.9003-0.03840.09760.10440.0332-0.2070.01450.04910.22310.24540.0743-0.02740.04830.14830.06530.09279.64153.8014-26.9947
30.1536-0.1803-0.08340.2874-0.05470.39330.007-0.0081-0.0098-0.0476-0.01960.010.07530.01590.01260.0340.0029-0.01030.06570.00110.0097-18.61592.5448-18.438
40.7407-0.04290.50530.3019-0.25050.51840.05670.04170.03440.01040.02050.11940.05520.0089-0.07710.0656-0.0054-0.00840.05920.01030.056-25.13749.5972-20.8097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 90
2X-RAY DIFFRACTION2ALLA91 - 137
3X-RAY DIFFRACTION3ALLB1 - 87
4X-RAY DIFFRACTION4ALLB88 - 137

+
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