[English] 日本語
Yorodumi
- PDB-9gku: Crystal Structure of Propanil hydrolase (PrpH) from Sphingomonas ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gku
TitleCrystal Structure of Propanil hydrolase (PrpH) from Sphingomonas sp. Y57
ComponentsPropanil hydrolase
KeywordsHYDROLASE / Deacetylase / Deacylase / Propanil hydrolase
Function / homology
Function and homology information


: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
ACETATE ION / beta-D-glucopyranose / : / Propanil hydrolase
Similarity search - Component
Biological speciesSphingomonas sp. Y57 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGraf, L.G. / Lammers, L. / Palm, G.J. / Schulze, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984/6-1 Germany
German Research Foundation (DFG)LA2984/8-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Distribution and diversity of classical deacylases in bacteria.
Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. ...Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. / Albrecht, D. / Zuhlke, D. / Sievers, S. / Strugnell, R.A. / Olsen, C.A. / Hofmann, K. / Lammers, M.
History
DepositionAug 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Propanil hydrolase
B: Propanil hydrolase
C: Propanil hydrolase
D: Propanil hydrolase
E: Propanil hydrolase
F: Propanil hydrolase
G: Propanil hydrolase
H: Propanil hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,75441
Polymers331,8248
Non-polymers2,93033
Water38,0842114
1
A: Propanil hydrolase
hetero molecules

D: Propanil hydrolase
hetero molecules

F: Propanil hydrolase
hetero molecules

H: Propanil hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,10719
Polymers165,9124
Non-polymers1,19515
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_566x,y+1,z+11
crystal symmetry operation1_455x-1,y,z1
2
C: Propanil hydrolase
E: Propanil hydrolase
hetero molecules

B: Propanil hydrolase
G: Propanil hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,64722
Polymers165,9124
Non-polymers1,73518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Unit cell
Length a, b, c (Å)103.861, 103.698, 104.499
Angle α, β, γ (deg.)113.603, 92.995, 120.605
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein / Sugars , 2 types, 17 molecules ABCDEFGH

#1: Protein
Propanil hydrolase


Mass: 41477.980 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion-protein / Source: (gene. exp.) Sphingomonas sp. Y57 (bacteria) / Strain: Y57 / Gene: prpH / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3JWV8
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 2138 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2114 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4% tacsimate pH 6 12% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.48→90.569 Å / Num. obs: 493656 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.64 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.076 / Rsym value: 0.064 / Χ2: 0.79 / Net I/σ(I): 9.1
Reflection shellResolution: 1.48→1.57 Å / Num. unique obs: 56793 / CC1/2: 0.665 / % possible all: 64.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSversion february 5, 2021data reduction
XDSversion february 5, 2021data scaling
PHASERv3.55.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→44.56 Å / SU ML: 0.1665 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.2296
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 24840 5.03 %
Rwork0.173 468519 -
obs0.1743 493359 91.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.53 Å2
Refinement stepCycle: LAST / Resolution: 1.48→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22615 0 156 2114 24885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005423443
X-RAY DIFFRACTIONf_angle_d0.850331907
X-RAY DIFFRACTIONf_chiral_restr0.07663509
X-RAY DIFFRACTIONf_plane_restr0.00774223
X-RAY DIFFRACTIONf_dihedral_angle_d17.58398664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.46861740.46733648X-RAY DIFFRACTION21.25
1.5-1.520.40944650.39738603X-RAY DIFFRACTION50.1
1.52-1.530.35516700.352813355X-RAY DIFFRACTION78.12
1.53-1.550.33877820.321115691X-RAY DIFFRACTION90.87
1.55-1.570.33488080.298415895X-RAY DIFFRACTION92.63
1.57-1.60.32948100.288716240X-RAY DIFFRACTION94.48
1.6-1.620.3188620.282616231X-RAY DIFFRACTION94.99
1.62-1.640.29749270.274216286X-RAY DIFFRACTION95.2
1.64-1.670.28659650.250116276X-RAY DIFFRACTION95.32
1.67-1.70.26549220.234216250X-RAY DIFFRACTION95.54
1.7-1.720.24558850.223616387X-RAY DIFFRACTION95.7
1.72-1.760.23679100.218716435X-RAY DIFFRACTION95.76
1.76-1.790.24839260.212116395X-RAY DIFFRACTION95.96
1.79-1.830.24099200.205516350X-RAY DIFFRACTION96.04
1.83-1.870.23549460.200516446X-RAY DIFFRACTION96.06
1.87-1.910.23089120.205616464X-RAY DIFFRACTION96.47
1.91-1.960.23719290.199516476X-RAY DIFFRACTION96.52
1.96-2.010.2189470.183816526X-RAY DIFFRACTION96.49
2.01-2.070.21328830.177616603X-RAY DIFFRACTION97.03
2.07-2.140.2148660.181116563X-RAY DIFFRACTION96.71
2.14-2.210.20828450.176516705X-RAY DIFFRACTION97.06
2.21-2.30.18558540.168316593X-RAY DIFFRACTION96.77
2.3-2.410.20058790.165416575X-RAY DIFFRACTION96.58
2.41-2.530.20079650.171416334X-RAY DIFFRACTION95.84
2.53-2.690.20398740.168316129X-RAY DIFFRACTION94.25
2.69-2.90.19317170.171116584X-RAY DIFFRACTION95.97
2.9-3.190.19977220.170116820X-RAY DIFFRACTION97.31
3.19-3.650.18087040.155416830X-RAY DIFFRACTION97.15
3.65-4.60.15477860.132716576X-RAY DIFFRACTION96.17
4.6-44.560.14829850.14116253X-RAY DIFFRACTION95.39

+
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