[English] 日本語
Yorodumi
- PDB-5zcg: Crystal structure of OsPP2C50 S265L/I267V:OsPYL/RCAR3 with (+)-ABA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zcg
TitleCrystal structure of OsPP2C50 S265L/I267V:OsPYL/RCAR3 with (+)-ABA
Components
  • ABA receptor RCAR3
  • Probable protein phosphatase 2C 50
KeywordsPLANT PROTEIN / abscisic acid / ABA / receptor / phosphatase / stress / complex
Function / homology
Function and homology information


regulation of intracellular signal transduction / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...regulation of intracellular signal transduction / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / response to cold / signaling receptor activity / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sigma factor PP2C-like phosphatases / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain ...Sigma factor PP2C-like phosphatases / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / Abscisic acid receptor PYL3 / Abscisic acid receptor PYL3 / Protein phosphatase 2C 50
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Oryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, S. / Han, S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
the Rural Development AgencyPJ013676 Korea, Republic Of
the National Research Foundation of KoreaNRF-2017R1D1A1B03032185 Korea, Republic Of
the National Research Foundation of KoreaSRC-2017R1A5A1014560 Korea, Republic Of
CitationJournal: Plant Mol.Biol. / Year: 2019
Title: Comprehensive survey of the VxG Phi L motif of PP2Cs from Oryza sativa reveals the critical role of the fourth position in regulation of ABA responsiveness.
Authors: Han, S. / Lee, J.Y. / Lee, Y. / Kim, T.H. / Lee, S.
History
DepositionFeb 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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.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
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Probable protein phosphatase 2C 50
B: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,92910
Polymers111,3034
Non-polymers6266
Water9,350519
1
A: Probable protein phosphatase 2C 50
C: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9645
Polymers55,6522
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-27 kcal/mol
Surface area20650 Å2
MethodPISA
2
B: Probable protein phosphatase 2C 50
D: ABA receptor RCAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9645
Polymers55,6522
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-29 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.738, 76.351, 77.942
Angle α, β, γ (deg.)62.96, 72.04, 66.93
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Probable protein phosphatase 2C 50 / OsPP2C50


Mass: 35590.645 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A/S265L/I267V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os05g0537400, LOC_Os05g46040, OJ1741_B01.18, OSJNBa0052K01.2
Production host: Escherichia coli (E. coli)
References: UniProt: Q6L5H6, protein-serine/threonine phosphatase
#2: Protein ABA receptor RCAR3


Mass: 20060.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: K4N2F7, UniProt: Q6EN42*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 2 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 7.5% PEG 3350, 80mM ammonium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→32.95 Å / Num. obs: 89408 / % possible obs: 95.82 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0675 / Rpim(I) all: 0.04617 / Net I/σ(I): 16.61
Reflection shellResolution: 1.97→2.041 Å / Rmerge(I) obs: 0.3323 / Num. unique obs: 7413 / CC1/2: 0.912 / Rpim(I) all: 0.2208

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWP

5gwp


Resolution: 2.1→32.946 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1616 2.25 %
Rwork0.202 --
obs0.2028 71944 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7315 0 42 519 7876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047497
X-RAY DIFFRACTIONf_angle_d0.93110150
X-RAY DIFFRACTIONf_dihedral_angle_d6.5974572
X-RAY DIFFRACTIONf_chiral_restr0.1021154
X-RAY DIFFRACTIONf_plane_restr0.0051326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16180.35921260.26255460X-RAY DIFFRACTION87
2.1618-2.23150.30371310.24565618X-RAY DIFFRACTION89
2.2315-2.31130.29031310.23345729X-RAY DIFFRACTION91
2.3113-2.40380.26171300.22635749X-RAY DIFFRACTION92
2.4038-2.51320.25461380.21515886X-RAY DIFFRACTION93
2.5132-2.64560.24321360.2115901X-RAY DIFFRACTION95
2.6456-2.81130.21861370.20586013X-RAY DIFFRACTION96
2.8113-3.02820.24521390.20386019X-RAY DIFFRACTION96
3.0282-3.33270.2211370.20046041X-RAY DIFFRACTION96
3.3327-3.81430.25571390.18995999X-RAY DIFFRACTION95
3.8143-4.80330.19911320.17715837X-RAY DIFFRACTION93
4.8033-32.95020.22131400.20096076X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 39.895 Å / Origin y: 15.6373 Å / Origin z: -7.8482 Å
111213212223313233
T0.2118 Å20.0011 Å2-0.0015 Å2-0.1964 Å2-0.0145 Å2--0.1856 Å2
L0.4738 °2-0.0224 °20.1503 °2-0.427 °20.1549 °2--0.5045 °2
S-0.009 Å °-0.022 Å °0.0089 Å °-0.0488 Å °0.003 Å °-0.0182 Å °-0.0139 Å °-0.0148 Å °0.0064 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