[English] 日本語
Yorodumi
- PDB-5z7w: Crystal structure of Striga hermonthica HTL1 (ShHTL1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z7w
TitleCrystal structure of Striga hermonthica HTL1 (ShHTL1)
ComponentsHyposensitive to light 1
KeywordsHYDROLASE / Hydrolase Activity / putative receptor of karrikin
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 1
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.657 Å
AuthorsXu, Y. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan Japan
Core Research for Evolutional Science and Technology Program of Japan Science and Technology Agency Japan
Grant-in-Aid for Scientific Research on Innovative Areas from the Japan Society for the Promotion of Science (JSPS)JP17H05835 Japan
JSPS KAKENHIJP15H05621 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga.
Authors: Xu, Y. / Miyakawa, T. / Nosaki, S. / Nakamura, A. / Lyu, Y. / Nakamura, H. / Ohto, U. / Ishida, H. / Shimizu, T. / Asami, T. / Tanokura, M.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hyposensitive to light 1
B: Hyposensitive to light 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,11810
Polymers60,7912
Non-polymers3268
Water14,736818
1
A: Hyposensitive to light 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5595
Polymers30,3961
Non-polymers1644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hyposensitive to light 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5585
Polymers30,3961
Non-polymers1624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.170, 138.770, 49.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-644-

HOH

31A-710-

HOH

41A-730-

HOH

51A-733-

HOH

61A-777-

HOH

-
Components

#1: Protein Hyposensitive to light 1 / Hydrolase / alpha/beta fold family protein


Mass: 30395.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M4AV81
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 818 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl (pH 8.5), 200mM MgCl2, 30% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.657→50 Å / Num. obs: 127266 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 18
Reflection shellResolution: 1.657→1.7 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8897 / CC1/2: 0.818 / Rrim(I) all: 0.875 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JYP

4jyp


Resolution: 1.657→38.953 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.1993 6415 5.04 %
Rwork0.1692 --
obs0.1708 127260 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.657→38.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 18 819 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044316
X-RAY DIFFRACTIONf_angle_d0.6575890
X-RAY DIFFRACTIONf_dihedral_angle_d12.7232544
X-RAY DIFFRACTIONf_chiral_restr0.05678
X-RAY DIFFRACTIONf_plane_restr0.005757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.657-1.67590.31052220.27983540X-RAY DIFFRACTION89
1.6759-1.69560.25661530.26784045X-RAY DIFFRACTION97
1.6956-1.71630.30081740.25273957X-RAY DIFFRACTION98
1.7163-1.7380.28282260.2484010X-RAY DIFFRACTION99
1.738-1.76090.24292230.23374077X-RAY DIFFRACTION100
1.7609-1.7850.26162020.22884030X-RAY DIFFRACTION100
1.785-1.81050.25942230.21534045X-RAY DIFFRACTION100
1.8105-1.83750.28792200.2194022X-RAY DIFFRACTION100
1.8375-1.86620.24452380.19784048X-RAY DIFFRACTION100
1.8662-1.89680.22842140.19394079X-RAY DIFFRACTION100
1.8968-1.92950.21812030.20484023X-RAY DIFFRACTION100
1.9295-1.96460.25381850.2044086X-RAY DIFFRACTION100
1.9646-2.00240.20822360.19464005X-RAY DIFFRACTION100
2.0024-2.04330.22351780.18844111X-RAY DIFFRACTION100
2.0433-2.08770.25561830.17784084X-RAY DIFFRACTION100
2.0877-2.13620.21022430.17624078X-RAY DIFFRACTION100
2.1362-2.18970.18122040.16944011X-RAY DIFFRACTION100
2.1897-2.24890.21782300.16364074X-RAY DIFFRACTION100
2.2489-2.3150.20142110.16984023X-RAY DIFFRACTION100
2.315-2.38970.21372160.16614066X-RAY DIFFRACTION100
2.3897-2.47510.19132280.16644063X-RAY DIFFRACTION100
2.4751-2.57420.19712620.16354005X-RAY DIFFRACTION100
2.5742-2.69140.20352230.17073997X-RAY DIFFRACTION100
2.6914-2.83320.19582420.16684044X-RAY DIFFRACTION100
2.8332-3.01070.16232120.15624048X-RAY DIFFRACTION100
3.0107-3.2430.1641860.14954082X-RAY DIFFRACTION100
3.243-3.56920.18362190.15074048X-RAY DIFFRACTION100
3.5692-4.08510.16782440.14184019X-RAY DIFFRACTION100
4.0851-5.1450.16042180.13824045X-RAY DIFFRACTION100
5.145-38.9640.20511970.16544080X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.6835 Å / Origin y: 25.3781 Å / Origin z: 15.3325 Å
111213212223313233
T0.0867 Å2-0.0017 Å20.0059 Å2-0.086 Å20.008 Å2--0.0571 Å2
L0.2793 °2-0.0576 °2-0.0115 °2-0.2991 °20.0606 °2--0.0174 °2
S0.0004 Å °0.007 Å °-0.0296 Å °0.0105 Å °-0.0069 Å °-0.0124 Å °-0.011 Å °-0.0007 Å °0 Å °
Refinement TLS groupSelection details: all

+
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