[English] 日本語
Yorodumi
- PDB-8rnn: Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rnn
TitleUnspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with prednisone
ComponentsUnspecific peroxygenase
KeywordsOXIDOREDUCTASE / Peroxygenase / peroxidase / complex / prednisone
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMarasmius wettsteinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsFernandez-Garcia, A. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSynergy CAM Project Y2018/BIO-4738-EVOQUIMERA-CM Spain
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Structural Insights and Reaction Profile of a New Unspecific Peroxygenase from Marasmius wettsteinii Produced in a Tandem-Yeast Expression System.
Authors: Sanchez-Moreno, I. / Fernandez-Garcia, A. / Mateljak, I. / Gomez de Santos, P. / Hofrichter, M. / Kellner, H. / Sanz-Aparicio, J. / Alcalde, M.
History
DepositionJan 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Unspecific peroxygenase
B: Unspecific peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,41928
Polymers51,7982
Non-polymers4,62126
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA-dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-129 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.126, 76.126, 186.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein / Sugars , 2 types, 8 molecules AB

#1: Protein Unspecific peroxygenase


Mass: 25899.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius wettsteinii (fungus) / Production host: Komagataella phaffii CBS 7435 (fungus) / References: unspecific peroxygenase
#2: 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.: 6
Source method: isolated from a genetically manipulated source
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 , 8 types, 594 molecules

#3: 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
#4: Chemical ChemComp-PDN / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / PREDNISONE / 1,4 PREGNADIENE-17ALPHA,21-DIOL-3,11,20-TRIONE / 1-CORTISONE / DEHYDROCORTISONE


Mass: 358.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 14% PEG 4000, 200mM ammonium sulfate. Soaking: 10mM prednisone, 5h30, cryoprotected with 15% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2021 / Details: KB MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.58→46.68 Å / Num. obs: 74091 / % possible obs: 98 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Χ2: 0.84 / Net I/σ(I): 19.4
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3697 / CC1/2: 0.969 / Rpim(I) all: 0.187 / Rrim(I) all: 0.495 / Χ2: 0.53 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→46.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.552 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21842 3655 4.9 %RANDOM
Rwork0.18186 ---
obs0.1836 70262 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.005 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.58→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 31 574 4515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124097
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163786
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6965638
X-RAY DIFFRACTIONr_angle_other_deg0.5031.5918748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.694533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54710607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024790
X-RAY DIFFRACTIONr_gen_planes_other0.010.02892
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_it1.3582.2831940
X-RAY DIFFRACTIONr_mcbond_other1.3472.2821940
X-RAY DIFFRACTIONr_mcangle_it2.0524.1072427
X-RAY DIFFRACTIONr_mcangle_other2.0534.1092428
X-RAY DIFFRACTIONr_scbond_it2.0522.5772157
X-RAY DIFFRACTIONr_scbond_other2.0522.5782158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1334.6493201
X-RAY DIFFRACTIONr_long_range_B_refined4.36325.014800
X-RAY DIFFRACTIONr_long_range_B_other4.34924.394750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 251 -
Rwork0.318 5271 -
obs--99.44 %

+
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