[English] 日本語
Yorodumi
- PDB-4w7l: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICUL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w7l
TitleCRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. D168N MUTANT
ComponentsDye-decolorizing peroxidase
KeywordsOXIDOREDUCTASE / HEME / GLYCOPROTEIN
Function / homology
Function and homology information


dye decolorizing peroxidase / peroxidase / lactoperoxidase activity / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol
Similarity search - Function
: / DyP dimeric alpha+beta barrel domain / : / 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
PROTOPORPHYRIN IX CONTAINING FE / Dye-decolorizing peroxidase AauDyP1
Similarity search - Component
Biological speciesAuricularia auricula-judae (jelly ear fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: Biochem.J. / Year: 2015
Title: Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.
Authors: Linde, D. / Pogni, R. / Canellas, M. / Lucas, F. / Guallar, V. / Baratto, M.C. / Sinicropi, A. / Saez-Jimenez, V. / Coscolin, C. / Romero, A. / Medrano, F.J. / Ruiz-Duenas, F.J. / Martinez, A.T.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dye-decolorizing peroxidase
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4464
Polymers94,2132
Non-polymers1,2332
Water32,3911798
1
A: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7232
Polymers47,1061
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7232
Polymers47,1061
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.650, 56.260, 103.820
Angle α, β, γ (deg.)90.00, 117.81, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Dye-decolorizing peroxidase


Mass: 47106.316 Da / Num. of mol.: 2 / Fragment: UNP residues 62-509 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Auricularia auricula-judae (jelly ear fungus)
Gene: dyp1 / Production host: Escherichia coli (E. coli) / References: UniProt: I2DBY1, dye decolorizing peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1798 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00791 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 405267 / % possible obs: 91.5 % / Redundancy: 5.8 % / Net I/σ(I): 12.7
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.7 / % possible all: 54.3

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFV

4afv


Resolution: 1.05→37.714 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1498 20298 5.01 %
Rwork0.1308 --
obs0.1318 405142 91.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→37.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 86 1798 8516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016994
X-RAY DIFFRACTIONf_angle_d1.4329576
X-RAY DIFFRACTIONf_dihedral_angle_d14.3972473
X-RAY DIFFRACTIONf_chiral_restr0.0951058
X-RAY DIFFRACTIONf_plane_restr0.0091277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0442-1.05610.32132190.32134195X-RAY DIFFRACTION30
1.0561-1.06850.29913690.27886735X-RAY DIFFRACTION49
1.0685-1.08150.27064110.24058000X-RAY DIFFRACTION57
1.0815-1.09520.2524820.21279057X-RAY DIFFRACTION65
1.0952-1.10960.21375600.200410333X-RAY DIFFRACTION74
1.1096-1.12480.20446120.184211553X-RAY DIFFRACTION83
1.1248-1.14090.19616870.17212758X-RAY DIFFRACTION92
1.1409-1.15790.17837270.154613857X-RAY DIFFRACTION99
1.1579-1.1760.16857310.147413907X-RAY DIFFRACTION100
1.176-1.19530.17427350.141513964X-RAY DIFFRACTION100
1.1953-1.21590.16217340.134513963X-RAY DIFFRACTION100
1.2159-1.2380.1647340.136613927X-RAY DIFFRACTION100
1.238-1.26180.16277340.134413932X-RAY DIFFRACTION100
1.2618-1.28760.15787370.125213995X-RAY DIFFRACTION100
1.2876-1.31560.14687340.12413993X-RAY DIFFRACTION100
1.3156-1.34620.14247340.120513944X-RAY DIFFRACTION100
1.3462-1.37990.14597370.117313979X-RAY DIFFRACTION100
1.3799-1.41720.1367380.11414030X-RAY DIFFRACTION100
1.4172-1.45890.14367340.107713980X-RAY DIFFRACTION100
1.4589-1.5060.13077370.108813984X-RAY DIFFRACTION100
1.506-1.55980.13627370.10514019X-RAY DIFFRACTION100
1.5598-1.62230.13567350.10813995X-RAY DIFFRACTION100
1.6223-1.69610.13827380.110814005X-RAY DIFFRACTION100
1.6961-1.78550.13547380.11614034X-RAY DIFFRACTION100
1.7855-1.89740.1487360.125313974X-RAY DIFFRACTION100
1.8974-2.04390.1357430.123514096X-RAY DIFFRACTION100
2.0439-2.24950.1377400.121114036X-RAY DIFFRACTION100
2.2495-2.5750.1337430.12714111X-RAY DIFFRACTION100
2.575-3.24390.15557430.139414125X-RAY DIFFRACTION100
3.2439-37.73820.14687590.136814363X-RAY DIFFRACTION99

+
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