[English] 日本語
Yorodumi
- PDB-5dj5: Crystal structure of rice DWARF14 in complex with synthetic strig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dj5
TitleCrystal structure of rice DWARF14 in complex with synthetic strigolactone GR24
ComponentsProbable strigolactone esterase D14
KeywordsHYDROLASE / alpha/beta
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-GR2 / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhou, X.E. / Zhao, L.-H. / Yi, W. / Wu, Z.-S. / Liu, Y. / Kang, Y. / Hou, L. / de Waal, P.W. / Li, S. / Jiang, Y. ...Zhou, X.E. / Zhao, L.-H. / Yi, W. / Wu, Z.-S. / Liu, Y. / Kang, Y. / Hou, L. / de Waal, P.W. / Li, S. / Jiang, Y. / Melcher, K. / Xu, H.E.
Funding support United States, China, 10items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
National Natural Science Foundation of China (NSFC)NSFC 31300245 China
National Natural Science Foundation of China (NSFC)NSFC 91217311 China
Ministry of Science and Technology (MoST, China)2012ZX09301001 China
Ministry of Science and Technology (MoST, China)2012CB910403 China
Ministry of Science and Technology (MoST, China)2013CB910600 China
Ministry of Science and Technology (MoST, China)XDB08020303 China
Ministry of Science and Technology (MoST, China)2013ZX09507001 China
CitationJournal: Cell Res. / Year: 2015
Title: Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3.
Authors: Zhao, L.H. / Zhou, X.E. / Yi, W. / Wu, Z. / Liu, Y. / Kang, Y. / Hou, L. / de Waal, P.W. / Li, S. / Jiang, Y. / Scaffidi, A. / Flematti, G.R. / Smith, S.M. / Lam, V.Q. / Griffin, P.R. / ...Authors: Zhao, L.H. / Zhou, X.E. / Yi, W. / Wu, Z. / Liu, Y. / Kang, Y. / Hou, L. / de Waal, P.W. / Li, S. / Jiang, Y. / Scaffidi, A. / Flematti, G.R. / Smith, S.M. / Lam, V.Q. / Griffin, P.R. / Wang, Y. / Li, J. / Melcher, K. / Xu, H.E.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable strigolactone esterase D14
B: Probable strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8033
Polymers58,5052
Non-polymers2981
Water2,936163
1
A: Probable strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5512
Polymers29,2531
Non-polymers2981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable strigolactone esterase D14


Theoretical massNumber of molelcules
Total (without water)29,2531
Polymers29,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.400, 87.880, 118.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 29252.594 Da / Num. of mol.: 2 / Fragment: alpha/beta hydrolase residues 52-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-GR2 / (3E,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}methylidene)-3,3a,4,8b-tetrahydro-2H-indeno[1,2-b]furan-2-one


Mass: 298.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG8000, ethylene glycol / PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→41.202 Å / Num. all: 17932 / Num. obs: 17932 / % possible obs: 87.7 % / Redundancy: 6.8 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.148 / Rsym value: 0.136 / Net I/av σ(I): 5.222 / Net I/σ(I): 14.6 / Num. measured all: 121345
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.537.10.6541.11690323700.2560.6544.381.2
2.53-2.687.10.5111.41590322320.20.5115.180.8
2.68-2.8770.3791.91466421030.150.3796.581.5
2.87-3.16.60.2562.91323420140.1050.2568.883
3.1-3.396.20.18241197319400.0770.18211.285.9
3.39-3.795.40.1057.11026118910.0480.10516.192.3
3.79-4.386.30.06511.61146218220.0280.06525.599.2
4.38-5.377.50.05513.71184015760.0210.05530.9100
5.37-7.597.80.06212971012380.0230.06225.3100
7.59-41.2027.20.03421.153957460.0130.03441.499.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
MOSFLMdata reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IH9

4ih9


Resolution: 2.4→39.92 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1254 7.02 %
Rwork0.19 --
obs0.1924 17868 87.34 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 22 163 4301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084258
X-RAY DIFFRACTIONf_angle_d1.1475811
X-RAY DIFFRACTIONf_dihedral_angle_d12.7131533
X-RAY DIFFRACTIONf_chiral_restr0.123672
X-RAY DIFFRACTIONf_plane_restr0.006753

+
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