[English] 日本語
Yorodumi
- PDB-6j2r: Crystal structure of Striga hermonthica HTL8 (ShHTL8) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j2r
TitleCrystal structure of Striga hermonthica HTL8 (ShHTL8)
ComponentsHyposensitive to light 8
KeywordsPLANT PROTEIN / Striga hermonthica / HTL8
Function / homologyAlpha/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 / Hyposensitive to light 8
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, Y.Y. / Xi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21332004 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure and biochemical characterization of Striga hermonthica HYPO-SENSITIVE TO LIGHT 8 (ShHTL8) in strigolactone signaling pathway.
Authors: Zhang, Y. / Wang, D. / Shen, Y. / Xi, Z.
History
DepositionJan 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hyposensitive to light 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2122
Polymers30,1201
Non-polymers921
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.628, 83.483, 84.077
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Hyposensitive to light 8


Mass: 30120.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4APJ4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium formate, 20% (w/v) PEG 3500 and 0.1 M ADA pH 6.6
PH range: 5.5-7.5 / Temp details: 303

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.399→50 Å / Num. obs: 58744 / % possible obs: 95.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.038 / Rrim(I) all: 0.088 / Χ2: 0.98 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.4220.30820390.8260.2560.4041.01167.3
1.42-1.452.30.30923150.8670.2350.3911.05676
1.45-1.482.60.28125520.8850.2040.351.03784.2
1.48-1.5130.2527720.9150.1670.3031.12190.9
1.51-1.543.40.21828770.950.1320.2571.02194.9
1.54-1.584.10.21329740.9540.1150.2431.05998
1.58-1.625.40.19530510.9690.0910.2151.10799.9
1.62-1.665.60.17730300.9750.0810.1951.127100
1.66-1.715.60.15830510.9790.0720.1741.08199.8
1.71-1.765.50.14130280.9810.0650.1551.07799.9
1.76-1.8350.12930700.980.0620.1431.09799.7
1.83-1.95.60.11930650.9830.0540.1311.11699.9
1.9-1.995.60.10630630.9810.0490.1170.997100
1.99-2.095.40.09930520.9870.0460.1090.94399.9
2.09-2.225.10.09230690.9870.0450.1030.99699.9
2.22-2.395.70.08630890.9890.0390.0940.87499.9
2.39-2.635.50.07931240.990.0360.0870.82199.9
2.63-3.025.30.07630980.9910.0350.0840.79899.8
3.02-3.85.50.07131560.990.0330.0780.84199.7
3.8-105.10.06132690.9930.0290.0680.69697.9

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A9D

6a9d


Resolution: 1.4→30.161 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.79
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1862 2963 5.21 %
Rwork0.1711 --
obs0.1719 56868 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.68 Å2 / Biso mean: 19.2301 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.4→30.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 6 267 2342
Biso mean--23.59 32.14 -
Num. residues----267
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.42150.3511560.2473115742
1.4215-1.4460.2672770.2389158457
1.446-1.47230.22591120.2234198273
1.4723-1.50060.22151290.2157234585
1.5006-1.53120.21521300.1986251793
1.5312-1.56450.20741530.1922266897
1.5645-1.60090.19381570.1811273199
1.6009-1.6410.17831550.17442721100
1.641-1.68530.19391350.17112781100
1.6853-1.73490.19881690.17142695100
1.7349-1.79090.16871510.16872749100
1.7909-1.85490.18951600.17062766100
1.8549-1.92920.16441650.16232721100
1.9292-2.01690.16791620.15872764100
2.0169-2.12320.19071590.16052749100
2.1232-2.25620.16791510.16112789100
2.2562-2.43040.18841510.1612798100
2.4304-2.67480.18781550.1682782100
2.6748-3.06150.21041640.17632806100
3.0615-3.8560.16771290.15942862100
3.856-100.18011430.1765293897
Refinement TLS params.Method: refined / Origin x: 13.2178 Å / Origin y: -3.4967 Å / Origin z: -0.8207 Å
111213212223313233
T0.1047 Å20.002 Å2-0.0018 Å2-0.1305 Å20.0042 Å2--0.0662 Å2
L0.6702 °2-0.0507 °2-0.0856 °2-0.4457 °2-0.0527 °2--1.9543 °2
S-0.0111 Å °-0.0315 Å °-0.0059 Å °0.0341 Å °0.031 Å °-0.0177 Å °0.0108 Å °0.0145 Å °-0.0245 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 269
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 267

+
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://pdbjlvh1.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