[English] 日本語
Yorodumi
- PDB-7f5w: Conserved and divergent strigolactone signaling in Saccharum spon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f5w
TitleConserved and divergent strigolactone signaling in Saccharum spontaneum
ComponentsHigh tillering and dwarf 2 protein
KeywordsPLANT PROTEIN / hydrolase protein DWARF 14 SL RECEPTOR
Function / homologylysophospholipase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / High tillering and dwarf 2 protein
Function and homology information
Biological speciesSaccharum hybrid cultivar ROC22 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.654 Å
AuthorsZhao, Q.Q. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052 China
CitationJournal: Front Plant Sci / Year: 2021
Title: Identification of Conserved and Divergent Strigolactone Receptors in Sugarcane Reveals a Key Residue Crucial for Plant Branching Control.
Authors: Hu, A. / Zhao, Q. / Chen, L. / Zhao, J. / Wang, Y. / Feng, K. / Wu, L. / Xie, M. / Zhou, X. / Xiao, L. / Ming, Z. / Zhang, M. / Yao, R.
History
DepositionJun 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: High tillering and dwarf 2 protein
B: High tillering and dwarf 2 protein


Theoretical massNumber of molelcules
Total (without water)65,6112
Polymers65,6112
Non-polymers00
Water6,431357
1
A: High tillering and dwarf 2 protein


Theoretical massNumber of molelcules
Total (without water)32,8051
Polymers32,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: High tillering and dwarf 2 protein


Theoretical massNumber of molelcules
Total (without water)32,8051
Polymers32,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.810, 88.295, 118.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein High tillering and dwarf 2 protein


Mass: 32805.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharum hybrid cultivar ROC22 (plant)
Gene: HTD2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0D5NT23
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Magnesium chloride hexahydrate, 0.05 M TRIS hydrochloride pH 7.5, 5% v/v 2-Propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.65→70.81 Å / Num. obs: 110054 / % possible obs: 93.6 % / Redundancy: 6.144 % / Rrim(I) all: 0.115 / Net I/σ(I): 12.1
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.744 / Num. unique obs: 58049

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXK

3vxk


Resolution: 1.654→70.806 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 3790 3.44 %
Rwork0.1914 106264 -
obs0.1927 110054 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 28.3539 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.654→70.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4151 0 0 357 4508
Biso mean---36.89 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6544-1.67540.39821520.3477411698
1.6754-1.69740.41741400.3402415198
1.6974-1.72070.33151500.3167417399
1.7207-1.74520.35071530.3215424299
1.7452-1.77130.40011460.31344203100
1.7713-1.7990.31961510.29454203100
1.799-1.82850.35661530.28664223100
1.8285-1.860.35081530.2762418199
1.86-1.89380.27921480.25964173100
1.8938-1.93030.2965550.2523159938
1.9303-1.96970.25651500.23334263100
1.9697-2.01250.25431540.22924184100
2.0125-2.05930.25431280.2272360199
2.0593-2.11080.235310.201691891
2.1108-2.16790.19351500.19234183100
2.1679-2.23170.23931510.1954239100
2.2317-2.30370.25231510.19654197100
2.3037-2.38610.21441500.1794226100
2.3861-2.48160.25481430.19074195100
2.4816-2.59450.2021530.19034256100
2.5945-2.73130.22221520.1844240100
2.7313-2.90250.24791440.18644191100
2.9025-3.12660.20241520.17714220100
3.1266-3.44120.22791470.1717399699
3.4412-3.93910.21871320.1565366789
3.9391-4.96270.16131540.1414238100
4.9627-4.96650.17711470.168418699
Refinement TLS params.Method: refined / Origin x: 22.4898 Å / Origin y: 2.9856 Å / Origin z: -4.7336 Å
111213212223313233
T0.0834 Å20.0232 Å2-0.0113 Å2-0.1121 Å2-0.0221 Å2--0.1126 Å2
L0.1212 °20.135 °2-0.1864 °2-0.414 °2-0.1198 °2--0.472 °2
S-0.0489 Å °-0.0062 Å °-0.01 Å °-0.0506 Å °0.0513 Å °-0.0439 Å °0.1244 Å °0.0226 Å °0.0049 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 268
2X-RAY DIFFRACTION1allB1 - 268
3X-RAY DIFFRACTION1allS1 - 357

+
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