[English] 日本語
Yorodumi
- PDB-5zhs: Crystal structure of OsD14 in complex with covalently bound KK052 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zhs
TitleCrystal structure of OsD14 in complex with covalently bound KK052
ComponentsStrigolactone esterase D14
KeywordsHYDROLASE / Plant hormones / Plant signalling / Strigolactones / receptor
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KAT / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHirabayashi, K. / Miyakawa, T. / Tanokura, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06736 Japan
Japan Society for the Promotion of Science (JSPS)17J04676 Japan
Japan Society for the Promotion of Science (JSPS)17K15258 Japan
CitationJournal: Mol Plant / Year: 2019
Title: Triazole Ureas Covalently Bind to Strigolactone Receptor and Antagonize Strigolactone Responses.
Authors: Nakamura, H. / Hirabayashi, K. / Miyakawa, T. / Kikuzato, K. / Hu, W. / Xu, Y. / Jiang, K. / Takahashi, I. / Niiyama, R. / Dohmae, N. / Tanokura, M. / Asami, T.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2822
Polymers30,0241
Non-polymers2571
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11210 Å2
Unit cell
Length a, b, c (Å)48.970, 48.970, 192.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

21A-859-

HOH

-
Components

#1: Protein Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2


Mass: 30024.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: Escherichia coli (E. coli)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-KAT / (4-phenylpiperazin-1-yl)(1H-1,2,3-triazol-1-yl)methanone


Mass: 257.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 20000, HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 23, 2016
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.49→41.413 Å / Num. obs: 84082 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.3 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXK

3vxk


Resolution: 1.49→41.413 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.96
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 3671 4.37 %Random
Rwork0.1877 ---
obs0.1887 84082 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→41.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 14 280 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052107
X-RAY DIFFRACTIONf_angle_d0.932870
X-RAY DIFFRACTIONf_dihedral_angle_d12.15756
X-RAY DIFFRACTIONf_chiral_restr0.036330
X-RAY DIFFRACTIONf_plane_restr0.004371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.50970.30041360.25912904X-RAY DIFFRACTION96
1.5097-1.53030.29441400.25253160X-RAY DIFFRACTION100
1.5303-1.55220.30951440.24463016X-RAY DIFFRACTION100
1.5522-1.57540.27341460.24553198X-RAY DIFFRACTION100
1.5754-1.60.27641380.2313064X-RAY DIFFRACTION100
1.6-1.62620.22431450.22973104X-RAY DIFFRACTION100
1.6262-1.65430.29241380.22293046X-RAY DIFFRACTION100
1.6543-1.68430.25111440.22933150X-RAY DIFFRACTION100
1.6843-1.71670.27041360.21093056X-RAY DIFFRACTION100
1.7167-1.75180.22551420.21923181X-RAY DIFFRACTION100
1.7518-1.78990.2761390.21342989X-RAY DIFFRACTION100
1.7899-1.83150.22571360.213145X-RAY DIFFRACTION100
1.8315-1.87730.25061480.21983171X-RAY DIFFRACTION100
1.8773-1.92810.29821440.21933032X-RAY DIFFRACTION100
1.9281-1.98480.22891380.20373099X-RAY DIFFRACTION100
1.9848-2.04890.19741550.19813103X-RAY DIFFRACTION100
2.0489-2.12210.20151450.1913139X-RAY DIFFRACTION100
2.1221-2.2070.20961420.19073025X-RAY DIFFRACTION100
2.207-2.30750.21551440.18833121X-RAY DIFFRACTION100
2.3075-2.42910.21591360.18713108X-RAY DIFFRACTION100
2.4291-2.58130.19831420.1863115X-RAY DIFFRACTION100
2.5813-2.78060.21451370.18563064X-RAY DIFFRACTION100
2.7806-3.06030.21671430.18823125X-RAY DIFFRACTION100
3.0603-3.50290.19851400.17833122X-RAY DIFFRACTION100
3.5029-4.41250.17491360.15073081X-RAY DIFFRACTION100
4.4125-41.42910.15771370.15893093X-RAY DIFFRACTION100

+
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