[English] 日本語
Yorodumi
- PDB-9gnm: X-ray crystal structure of VvPYL1-ABA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gnm
TitleX-ray crystal structure of VvPYL1-ABA
ComponentsAbscisic acid receptor PYR1
KeywordsPLANT PROTEIN / VvPYL1 / ABA receptor protein
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRivera-Moreno, M. / Benavente, J.L. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: To Be Published
Title: Regulation of transpiration in grapevine through chemical activation of ABA signaling by ABA receptor agonists
Authors: Rivera-Moreno, M. / Benavente, J.L. / Infantes, L. / Albert, A.
History
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abscisic acid receptor PYR1
B: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3743
Polymers48,0912
Non-polymers2821
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area18210 Å2
Unit cell
Length a, b, c (Å)54.028, 69.417, 107.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 28 through 217)
d_2ens_1(chain "B" and resid 28 through 217)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 28 - 217 / Label seq-ID: 19 - 209

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.820085000928, -0.517833705159, -0.243534073704), (-0.520149507141, -0.851965735049, 0.0599906369572), (-0.238547859923, 0.0774767068444, -0.968035267138)Vector: -1. ...NCS oper: (Code: given
Matrix: (0.820085000928, -0.517833705159, -0.243534073704), (-0.520149507141, -0.851965735049, 0.0599906369572), (-0.238547859923, 0.0774767068444, -0.968035267138)
Vector: -1.91832128933, -4.85509005116, -10.0855454112)

-
Components

#1: Protein Abscisic acid receptor PYR1


Mass: 24045.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: VIT_02s0012g01270
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F6HT94
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, pH 5.0, 0.2 M magnesium chloride, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97912 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.1→42.64 Å / Num. obs: 24246 / % possible obs: 99.59 % / Redundancy: 1.34 % / Biso Wilson estimate: 34.49 Å2 / CC1/2: 0.946 / Net I/σ(I): 47.34
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2375 / CC1/2: 0.825 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.64 Å / SU ML: 0.308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2695 1212 5 %
Rwork0.2321 23010 -
obs0.234 24222 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 19 21 3076
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.28573697156 Å
LS refinement shellResolution: 2.1→2.18 Å / % reflection obs: 98.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5153485959730.2003317595820.01216150877040.4721541138580.3076121937580.0852838742021-0.0373646933288-0.0313142699794-0.0243289707613-0.09180909491760.09932063123310.042253776225-0.0789892957531-0.0285880561691-6.79017447965E-60.4037620978180.01048470321460.0136574763840.3042217359360.01073573220470.352475419247-3.72938920326-7.85656833461-24.7256569091
20.5715823625320.0605570388608-0.6375499979090.0917627435458-0.2701721692390.4348811825720.0319688462805-0.1451627251640.06859174330140.332806082641-0.0119069884355-0.158381122395-0.9543454792180.3951801766620.003790279176970.418834245351-0.0258101636089-0.002390305205760.423858836740.009924085200870.35023937896611.53059183687.57730712647-17.4751201259
30.7246771475950.336868137299-0.1294966158031.439662605370.2200724847980.674198358012-0.04881837658990.147031821122-0.09325248353560.03662812962440.04007451255840.00033473453904-0.1320149980470.147470695539-8.93667574821E-50.2788660486750.004966570282160.01797706320230.2993977656270.04464674844530.2858882185533.33556964565-2.78864565513-22.6055124243
40.483051798053-0.1312275619960.1139279541430.0877986760687-0.2385730702220.507078843693-0.0133400752263-0.41360297392-0.2862353415210.2720147770830.2440055895590.4786887851440.0586442537473-0.09704389627968.02541767811E-50.367341419267-0.04121732493910.02406392072230.2986827229420.04343842899850.356292902475-0.189545911824-2.9273121545-12.0588820127
50.3908835475590.0118593478380.0697641565934-0.0570449918566-0.2158729853250.2722912222430.11394193784-0.4972164120550.3307854292750.490858837556-0.08605793132790.190053692595-0.21638168325-0.0190908069228-0.0001791380626230.63137322294-0.003652073662940.003751636841710.360722180027-0.07150791103490.4782210705945.900185461316.8909077416416.4493826122
60.187710562254-0.01925258306160.194301364733-0.243687937665-0.1561012214220.2049843248910.034091758481-0.1293758335430.0379889322903-0.151722766659-0.05338290367650.0323505779151-0.1794027401340.0733174118171-0.0002445662208760.331891612909-0.0194399731097-0.03712506022080.385769404222-0.02468064205480.3655778724894.43112908981-2.3925872803611.2972787252
70.0697006991666-0.07415210824710.0262388223761-0.00536047171192-0.07343837719020.03660410027020.2311981734610.1427685581510.00873694995305-0.1545828216850.05378264058330.5962488361820.474714293276-0.103718744668-0.0001718734996820.475838218802-0.108464086479-0.03014687128120.375042704260.045673167140.436210076662.49904294953-14.41634444134.30460247666
80.267104322061-0.03840518109910.1169085779120.08413996821860.05802720307830.08425582258610.02290840353230.0422212417107-0.204536758754-0.1939016395190.2936344584330.2492998647170.615777760669-0.5299758117240.0009441996469130.6153966951760.0408632918749-0.002221635219930.3596054468590.02342492838090.4669579646697.41341009845-22.80966607339.53441230101
90.6295570301440.1193139705040.4800346745870.0703248251818-0.02802328416110.4918035618560.1017218935840.0620729703105-0.03314344696570.331748676104-0.1982717206590.07597828195760.5964065824180.0752577615548-0.006701980165350.4860902248070.0340070547365-0.02545789933870.3621599141170.01671193951550.35020664425510.4745800979-14.32224853978.55844508639
100.7264059793770.3109524619160.5611582363410.90121100412-0.2188882662290.9341834987680.0229576054868-0.3056804758570.1629838990660.156114440536-0.0180171424583-0.04028533555720.106958982930.122701336518-6.82002436151E-50.278682982955-0.02764484904590.005301143427940.35879342687-0.02106434067090.3329480529087.63960767469-1.972186922189.19015627591
110.409482568361-0.19994417744-0.0152490308976-0.07913182160140.02055138896930.1966187500360.3025024259390.1182755388290.2280458044550.0791892404394-0.1794287525830.0596174332772-0.1193617388260.0577557489078-0.000192103934010.423851031375-0.0120749402781-0.010402185590.372301296540.02677934191040.3211470814993.31249363687-2.476534880491.50807899752
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 86 )AA28 - 861 - 59
22chain 'A' and (resid 87 through 127 )AA87 - 12760 - 100
33chain 'A' and (resid 128 through 189 )AA128 - 189101 - 162
44chain 'A' and (resid 190 through 219 )AA190 - 219163 - 192
55chain 'B' and (resid 28 through 57 )BB28 - 571 - 30
66chain 'B' and (resid 58 through 86 )BB58 - 8631 - 59
77chain 'B' and (resid 87 through 98 )BB87 - 9860 - 71
88chain 'B' and (resid 99 through 114 )BB99 - 11472 - 87
99chain 'B' and (resid 115 through 149 )BB115 - 14988 - 122
1010chain 'B' and (resid 150 through 189 )BB150 - 189123 - 162
1111chain 'B' and (resid 190 through 217 )BB190 - 217163 - 190

+
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