[English] 日本語
Yorodumi
- PDB-8qd7: Wdyg1p from W. dermatitidis catalyzes polyketide shortening in th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qd7
TitleWdyg1p from W. dermatitidis catalyzes polyketide shortening in the biosynthesis of DHN-melanin
ComponentsYellowish-green 1-like protein
KeywordsLYASE / Natural Product Biosynthesis / Polyketide Synthase System / alpha / beta-Hydrolase Fold / Polyketide Shortening / Retro Claisen Reaction
Function / homologyEsterase FrsA-like / Esterase FrsA-like / : / Alpha/Beta hydrolase fold / Yellowish-green 1-like protein
Function and homology information
Biological speciesExophiala dermatitidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: Adv Sci / Year: 2024
Title: Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments.
Authors: Schmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M.
History
DepositionAug 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Yellowish-green 1-like protein
B: Yellowish-green 1-like protein


Theoretical massNumber of molelcules
Total (without water)98,4602
Polymers98,4602
Non-polymers00
Water10,845602
1
A: Yellowish-green 1-like protein


Theoretical massNumber of molelcules
Total (without water)49,2301
Polymers49,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Yellowish-green 1-like protein


Theoretical massNumber of molelcules
Total (without water)49,2301
Polymers49,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.020, 86.620, 115.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Yellowish-green 1-like protein


Mass: 49230.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exophiala dermatitidis (fungus) / Gene: yg1 / Plasmid: pCDFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6BCB5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM tris, 22-25% PEG 3350 / PH range: 8.0-9.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 65754 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9449 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→48.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.957 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19701 3287 5 %RANDOM
Rwork0.15665 ---
obs0.15864 62450 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.762 Å2
Baniso -1Baniso -2Baniso -3
1-27.02 Å20 Å20 Å2
2---21.15 Å2-0 Å2
3----5.87 Å2
Refinement stepCycle: 1 / Resolution: 1.85→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 0 602 7177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136768
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166295
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.6449173
X-RAY DIFFRACTIONr_angle_other_deg1.1741.5814597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74722.8325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.609151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3721530
X-RAY DIFFRACTIONr_chiral_restr0.0550.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021494
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_it0.6871.5763315
X-RAY DIFFRACTIONr_mcbond_other0.6871.5763314
X-RAY DIFFRACTIONr_mcangle_it0.9512.3654142
X-RAY DIFFRACTIONr_mcangle_other0.9512.3664143
X-RAY DIFFRACTIONr_scbond_it0.7381.7113453
X-RAY DIFFRACTIONr_scbond_other0.7381.7113453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9522.5125031
X-RAY DIFFRACTIONr_long_range_B_refined1.77619.7258025
X-RAY DIFFRACTIONr_long_range_B_other1.60119.1547884
X-RAY DIFFRACTIONr_rigid_bond_restr0.502313063
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 239 -
Rwork0.172 4544 -
obs--98.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7179-0.2119-0.130.75460.33390.81920.0070.0748-0.0149-0.0505-0.0127-0.01950.0040.06450.00570.0054-0.00550.00040.09170.00650.1031-0.97229.147-11.041
20.4559-0.16950.0031.20120.11310.8579-0.0674-0.06090.02890.16630.0715-0.0642-0.1143-0.0392-0.00410.07130.0209-0.04570.1074-0.01130.1265-3.62768.96712.382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 413
2X-RAY DIFFRACTION2B0 - 412

+
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