[English] 日本語
Yorodumi
- PDB-3mm3: Dye-decolorizing peroxidase (DyP) D171N in complex with cyanide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mm3
TitleDye-decolorizing peroxidase (DyP) D171N in complex with cyanide
ComponentsDyP
KeywordsOXIDOREDUCTASE / DyP / Dye-decolorizing peroxidase / beta barrel / aspartic acid
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / DyP dimeric alpha+beta barrel domain / : / Dyp-type peroxidase, C-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / DyP
Similarity search - Component
Biological speciesBjerkandera adusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSugano, Y. / Yoshida, T. / Tsuge, H.
CitationJournal: Febs J. / Year: 2011
Title: The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
Authors: Yoshida, T. / Tsuge, H. / Konno, H. / Hisabori, T. / Sugano, Y.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references / Source and taxonomy
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1393
Polymers47,4961
Non-polymers6432
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.954, 97.150, 46.460
Angle α, β, γ (deg.)90.000, 104.040, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DyP / dye-decolorizing peroxidase


Mass: 47496.355 Da / Num. of mol.: 1 / Fragment: residues in UNP 57-498 / Mutation: D171N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bjerkandera adusta (fungus) / Gene: dyp / Plasmid: pTAex3 / Production host: Aspergillus oryzae (mold) / Strain (production host): M-2-3 / References: UniProt: Q8WZK8, dye decolorizing peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.64 % / Mosaicity: 0.709 °
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, pH 6.0, vapor diffusion, hanging drop, temperature 278K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 75208 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Χ2: 1.847 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.423.60.26136821.561198
1.42-1.453.70.23837621.566198.2
1.45-1.483.70.21336901.623198.3
1.48-1.513.70.18937271.676198.5
1.51-1.543.70.17437241.687198.4
1.54-1.583.70.15337301.753198.9
1.58-1.623.70.13737551.756198.8
1.62-1.663.70.12237931.843199
1.66-1.713.70.10937271.868199.1
1.71-1.763.80.09337351.823199.2
1.76-1.833.80.08237651.881199.4
1.83-1.93.80.07137811.978199.4
1.9-1.993.80.06337731.996199.6
1.99-2.093.80.05538091.998199.8
2.09-2.223.80.05237922.062199.9
2.22-2.393.80.04737971.989199.9
2.39-2.633.80.04338181.9591100
2.63-3.023.80.03938101.923199.9
3.02-3.83.70.03537922.014199.2
3.8-503.60.03237461.938196.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å28.93 Å
Translation3 Å28.93 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D3Q

2d3q


Resolution: 1.4→48.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.897 / SU B: 0.818 / SU ML: 0.034 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3785 5 %RANDOM
Rwork0.181 ---
obs0.182 75184 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 34.27 Å2 / Biso mean: 11.256 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20.05 Å2
2---0.59 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 45 153 3536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223476
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9844756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1424.908163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4415495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6691516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212764
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5871.52183
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10423519
X-RAY DIFFRACTIONr_scbond_it1.61231293
X-RAY DIFFRACTIONr_scangle_it2.5114.51237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 269 -
Rwork0.234 5066 -
all-5335 -
obs--96.07 %

+
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