[English] 日本語
Yorodumi
- PDB-5mob: ABA RECEPTOR FROM TOMATO, SlPYL1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mob
TitleABA RECEPTOR FROM TOMATO, SlPYL1
ComponentsSlPYL1_ABA
KeywordsSIGNALING PROTEIN / ABA / RECEPTOR / SIGNALING / STRESS
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta / Chem-A8S / :
Function and homology information
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.669 Å
AuthorsMoreno-Alvero, M. / Yunta, C. / Gonzalez-Guzman, M. / Arbona, V. / Granell, A. / Martinez-Ripoll, M. / Infantes, L. / Rodriguez, P.L. / Albert, A.
CitationJournal: Mol Plant / Year: 2017
Title: Structure of Ligand-Bound Intermediates of Crop ABA Receptors Highlights PP2C as Necessary ABA Co-receptor.
Authors: Moreno-Alvero, M. / Yunta, C. / Gonzalez-Guzman, M. / Lozano-Juste, J. / Benavente, J.L. / Arbona, V. / Menendez, M. / Martinez-Ripoll, M. / Infantes, L. / Gomez-Cadenas, A. / Rodriguez, P.L. / Albert, A.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SlPYL1_ABA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0993
Polymers25,7381
Non-polymers3602
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 87.470, 55.751
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein SlPYL1_ABA


Mass: 25738.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli (E. coli) / References: UniProt: K4CN56
#2: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 3.5 M de sulfato de amonio pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.67→28.63 Å / Num. obs: 27365 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.99 / Net I/σ(I): 17.1
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.1 % / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
Aimlessv7.0data scaling
SCALAv7.0data scaling
MOLREPv7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.669→28.631 Å / SU ML: 0.41 / Cross valid method: NONE / σ(F): 0.69 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2827 5.11 %
Rwork0.1914 --
obs0.193 55376 99.83 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.757 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.797 Å20 Å20 Å2
2---9.797 Å2-0 Å2
3---19.5941 Å2
Refinement stepCycle: LAST / Resolution: 1.669→28.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 24 168 1711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061575
X-RAY DIFFRACTIONf_angle_d1.0012147
X-RAY DIFFRACTIONf_dihedral_angle_d16.878578
X-RAY DIFFRACTIONf_chiral_restr0.064249
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6691-1.69790.38451590.37162585X-RAY DIFFRACTION99
1.6979-1.72880.37021270.35412654X-RAY DIFFRACTION100
1.7288-1.7620.33791400.32532610X-RAY DIFFRACTION100
1.762-1.7980.30591580.28652613X-RAY DIFFRACTION100
1.798-1.83710.28121270.25132650X-RAY DIFFRACTION100
1.8371-1.87980.27671250.24042643X-RAY DIFFRACTION100
1.8798-1.92680.29781740.2432593X-RAY DIFFRACTION100
1.9268-1.97890.22491390.1952626X-RAY DIFFRACTION100
1.9789-2.03710.25011310.17532656X-RAY DIFFRACTION100
2.0371-2.10280.22011300.17652620X-RAY DIFFRACTION100
2.1028-2.1780.21021610.18382637X-RAY DIFFRACTION100
2.178-2.26510.2441250.20062636X-RAY DIFFRACTION100
2.2651-2.36820.21981530.1782601X-RAY DIFFRACTION100
2.3682-2.4930.23281530.18182628X-RAY DIFFRACTION100
2.493-2.64910.25311360.19522668X-RAY DIFFRACTION100
2.6491-2.85340.25021320.19452619X-RAY DIFFRACTION100
2.8534-3.14030.24021530.19282640X-RAY DIFFRACTION100
3.1403-3.59390.20171590.18352587X-RAY DIFFRACTION100
3.5939-4.52510.16731340.14922656X-RAY DIFFRACTION100
4.5251-28.63540.17141110.17882627X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.5726 Å / Origin y: 15.1959 Å / Origin z: 3.8631 Å
111213212223313233
T0.2023 Å2-0.0004 Å2-0.0248 Å2-0.1982 Å2-0.0069 Å2--0.2043 Å2
L1.5786 °2-0.1065 °20.0134 °2-0.9748 °2-0.2317 °2--0.896 °2
S0.042 Å °-0.0139 Å °-0.1412 Å °-0.0148 Å °0.034 Å °0.0259 Å °0.0214 Å °0.007 Å °0.0004 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