[English] 日本語
Yorodumi
- PDB-7pn6: Evolved unspecific peroxygenase with A77L mutation in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pn6
TitleEvolved unspecific peroxygenase with A77L mutation in complex with myristic acid
ComponentsAromatic peroxygenase
KeywordsOXIDOREDUCTASE / Myristic acid complex / peroxygenase / peroxidase
Function / homology
Function and homology information


unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Chloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MYRISTIC ACID / PHOSPHATE ION / Aromatic peroxygenase
Similarity search - Component
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsFernandez-Garcia, A. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesComunidad de Madrid Synergy CAM project Y2018/BIO-4738-EVOCHIMERA-CM Spain
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids.
Authors: Gomez de Santos, P. / Gonzalez-Benjumea, A. / Fernandez-Garcia, A. / Aranda, C. / Wu, Y. / But, A. / Molina-Espeja, P. / Mate, D.M. / Gonzalez-Perez, D. / Zhang, W. / Kiebist, J. / ...Authors: Gomez de Santos, P. / Gonzalez-Benjumea, A. / Fernandez-Garcia, A. / Aranda, C. / Wu, Y. / But, A. / Molina-Espeja, P. / Mate, D.M. / Gonzalez-Perez, D. / Zhang, W. / Kiebist, J. / Scheibner, K. / Hofrichter, M. / Swiderek, K. / Moliner, V. / Sanz-Aparicio, J. / Hollmann, F. / Gutierrez, A. / Alcalde, M.
History
DepositionSep 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aromatic peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,09611
Polymers35,9901
Non-polymers2,10610
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-30 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.205, 57.908, 61.121
Angle α, β, γ (deg.)90.000, 109.460, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 6 molecules A

#1: Protein Aromatic peroxygenase / AaP


Mass: 35990.012 Da / Num. of mol.: 1 / Mutation: V57A, L67F, V75I, A77L, I248V, F311L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: APO1 / Production host: Komagataella phaffii CBS 7435 (fungus) / References: UniProt: B9W4V6, unspecific peroxygenase
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 227 molecules

#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.45M sodium potassium phosphate pH 5.6, 3% MPD Soaking: 10 mM myristic acid, 18 hours, cryoprotected with 25% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2020 / Details: KB MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→48.33 Å / Num. obs: 54034 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Χ2: 0.96 / Net I/σ(I): 15.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 2700 / Rpim(I) all: 0.274 / Rrim(I) all: 0.699 / Χ2: 0.92 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5OXU

5oxu


Resolution: 1.5→48.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.247 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 2658 4.9 %RANDOM
Rwork0.1627 ---
obs0.1639 51357 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.5 Å2 / Biso mean: 13.026 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20.23 Å2
2---0.65 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: final / Resolution: 1.5→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 136 222 2875
Biso mean--23.93 21.36 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132796
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172516
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.7243832
X-RAY DIFFRACTIONr_angle_other_deg1.5791.6255807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4821.961153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1451520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023263
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02691
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 203 -
Rwork0.188 3782 -
all-3985 -
obs--99.95 %

+
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