[English] 日本語
Yorodumi
- PDB-7z1p: X-ray crystal structure of SLPYL1-E151D mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z1p
TitleX-ray crystal structure of SLPYL1-E151D mutant
ComponentsSLPYL1-E151D
KeywordsPLANT PROTEIN / SLPYL1 / ABA receptor protein
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsInfantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: Front Plant Sci / Year: 2022
Title: Structure-Based Modulation of the Ligand Sensitivity of a Tomato Dimeric Abscisic Acid Receptor Through a Glu to Asp Mutation in the Latch Loop.
Authors: Infantes, L. / Rivera-Moreno, M. / Daniel-Mozo, M. / Benavente, J.L. / Ocana-Cuesta, J. / Coego, A. / Lozano-Juste, J. / Rodriguez, P.L. / Albert, A.
History
DepositionFeb 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: SLPYL1-E151D


Theoretical massNumber of molelcules
Total (without water)25,7241
Polymers25,7241
Non-polymers00
Water1,29772
1
A: SLPYL1-E151D

A: SLPYL1-E151D


Theoretical massNumber of molelcules
Total (without water)51,4492
Polymers51,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.969, 89.969, 51.768
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein SLPYL1-E151D


Mass: 25724.418 Da / Num. of mol.: 1 / Mutation: E151D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: 101268417 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q7HTY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate 1.8M

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979261 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979261 Å / Relative weight: 1
ReflectionResolution: 1.82→44.98 Å / Num. obs: 21962 / % possible obs: 99.76 % / Redundancy: 16.4 % / Biso Wilson estimate: 38.73 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05691 / Rpim(I) all: 0.01465 / Rrim(I) all: 0.05881 / Net I/σ(I): 23.84
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 16.3 % / Rmerge(I) obs: 1.979 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 2149 / CC1/2: 0.896 / Rpim(I) all: 0.4977 / Rrim(I) all: 2.042 / % possible all: 99.16

-
Processing

Software
NameVersionClassification
XDSVERSION Feb 5, 2021 BUILT=20210205data reduction
XDSVERSION Feb 5, 2021 BUILT=20210205data scaling
PHENIX1.20_4459refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MOA

5moa


Resolution: 1.82→44.98 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 1064 4.85 %
Rwork0.2094 20893 -
obs0.211 21957 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.06 Å2
Refinement stepCycle: LAST / Resolution: 1.82→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 72 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721552
X-RAY DIFFRACTIONf_angle_d0.97892115
X-RAY DIFFRACTIONf_chiral_restr0.0637250
X-RAY DIFFRACTIONf_plane_restr0.0106273
X-RAY DIFFRACTIONf_dihedral_angle_d5.3046211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.90.48411230.41062538X-RAY DIFFRACTION98.48
1.9-20.35151260.2882620X-RAY DIFFRACTION99.85
2-2.130.2911260.2562575X-RAY DIFFRACTION99.78
2.13-2.290.2451210.24862596X-RAY DIFFRACTION99.89
2.29-2.520.26991200.25132616X-RAY DIFFRACTION99.64
2.52-2.890.29531210.24982642X-RAY DIFFRACTION99.96
2.89-3.640.25721540.21592606X-RAY DIFFRACTION100
3.64-44.980.20221730.16352700X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 1.63014664679 Å / Origin y: 30.8149453295 Å / Origin z: -5.41587322678 Å
111213212223313233
T0.313368317976 Å2-0.0130397287979 Å2-0.00753404686905 Å2-0.344165274931 Å20.00826133946939 Å2--0.337117353158 Å2
L0.922671844513 °2-0.419884850228 °20.350254880519 °2-0.925057103091 °2-0.203138605218 °2--1.63986415715 °2
S0.00455620213387 Å °0.137051047672 Å °-0.203517117402 Å °0.0897403025823 Å °0.082784149221 Å °0.0953665419965 Å °0.0323136090489 Å °-0.0107782253217 Å °-3.84664070981E-6 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