[English] 日本語
Yorodumi
- PDB-7o9l: Dictyostelium discoideum dye decolorizing peroxidase DyPA in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o9l
TitleDictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.
ComponentsDyPA
KeywordsHYDROLASE / Dye decolorizing-type peroxidase / Dictyostelium discoideum / B-type DyP
Function / homology
Function and homology information


peroxidase activity / protein dimerization activity / heme binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRai, A. / Fedorov, R. / Manstein, D.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2155 - 39087428-B11 Germany
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum .
Authors: Rai, A. / Klare, J.P. / Reinke, P.Y.A. / Englmaier, F. / Fohrer, J. / Fedorov, R. / Taft, M.H. / Chizhov, I. / Curth, U. / Plettenburg, O. / Manstein, D.J.
History
DepositionApr 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DyPA
B: DyPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,57213
Polymers70,8532
Non-polymers1,71911
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-35 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.050, 141.050, 95.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein DyPA


Mass: 35426.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB0168077, DDB0217308 / Production host: Escherichia coli (E. coli) / References: UniProt: Q556V8
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 2.4 M Sodium malonate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91985 Å / Relative weight: 1
ReflectionResolution: 1.85→47.74 Å / Num. obs: 82374 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 25.87 Å2 / Rmerge(I) obs: 0.0394 / Net I/σ(I): 15.36
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 26.22 % / Rmerge(I) obs: 0.36 / Num. unique obs: 10792 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O9J

7o9j


Resolution: 1.85→45.22 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1799 4123 5.01 %
Rwork0.1546 78169 -
obs0.1559 82292 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 118 393 5429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075135
X-RAY DIFFRACTIONf_angle_d1.10266926
X-RAY DIFFRACTIONf_chiral_restr0.0773744
X-RAY DIFFRACTIONf_plane_restr0.005886
X-RAY DIFFRACTIONf_dihedral_angle_d12.1052711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.30171340.2682681X-RAY DIFFRACTION99.96
1.87-1.890.2441260.23982661X-RAY DIFFRACTION99.96
1.89-1.920.26391320.22392668X-RAY DIFFRACTION99.96
1.92-1.940.22681380.20392648X-RAY DIFFRACTION100
1.94-1.970.21411340.1822669X-RAY DIFFRACTION100
1.97-20.21841300.17212681X-RAY DIFFRACTION99.96
2-2.030.19031430.15912677X-RAY DIFFRACTION100
2.03-2.060.1481350.16132639X-RAY DIFFRACTION100
2.06-2.090.18181390.15652661X-RAY DIFFRACTION100
2.09-2.130.21081400.15172681X-RAY DIFFRACTION100
2.13-2.170.18891370.14432677X-RAY DIFFRACTION100
2.17-2.210.18411410.15262672X-RAY DIFFRACTION100
2.21-2.260.18741280.14922661X-RAY DIFFRACTION100
2.26-2.30.17831570.14962682X-RAY DIFFRACTION100
2.3-2.360.19661150.14542678X-RAY DIFFRACTION100
2.36-2.420.18941600.14952642X-RAY DIFFRACTION100
2.42-2.480.18231530.1542690X-RAY DIFFRACTION100
2.48-2.560.19231390.1592683X-RAY DIFFRACTION100
2.56-2.640.1961680.15472681X-RAY DIFFRACTION100
2.64-2.730.18741410.15252696X-RAY DIFFRACTION100
2.73-2.840.19841390.15912687X-RAY DIFFRACTION100
2.84-2.970.20061460.14732696X-RAY DIFFRACTION100
2.97-3.130.1961580.15482692X-RAY DIFFRACTION100
3.13-3.320.16691350.14932724X-RAY DIFFRACTION100
3.32-3.580.14771450.13692723X-RAY DIFFRACTION100
3.58-3.940.14861500.13352740X-RAY DIFFRACTION100
3.94-4.510.14711570.12962752X-RAY DIFFRACTION100
4.51-5.680.13651440.14642795X-RAY DIFFRACTION100
5.68-45.220.23121590.18762932X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 9.07372623191 Å / Origin y: 26.3872388582 Å / Origin z: 13.8894603174 Å
111213212223313233
T0.182983943672 Å20.000127154021361 Å20.0115782255618 Å2-0.163041026471 Å2-0.00265672933352 Å2--0.155973560617 Å2
L0.731010940556 °20.0356503521698 °20.191328614111 °2-0.399493735993 °2-0.0937732193032 °2--0.368476040866 °2
S0.0253977977697 Å °-0.0343060747996 Å °0.0184710285122 Å °0.0208194255957 Å °0.00183337730152 Å °0.0216513855796 Å °-0.0323598516211 Å °-0.00616214614121 Å °8.76512148177E-6 Å °
Refinement TLS groupSelection details: all

+
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