[English] 日本語
Yorodumi
- PDB-4psb: Crystal Structure of Phytohormone Binding Protein from Vigna radi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4psb
TitleCrystal Structure of Phytohormone Binding Protein from Vigna radiata in complex with gibberellic acid (GA3)
ComponentsCytokinin-specific binding protein
KeywordsPLANT PROTEIN / Cytokinin Specific Binding Protein (CSBP) / PR-10 FOLD / GIBBERELLIN / CYTOKININ / PLANT HORMONE BINDING
Function / homology
Function and homology information


gibberellin binding / cytokinin binding / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GIBBERELLIN A3 / Phytohormone-binding protein CSBP / Phytohormone-binding protein CSBP
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsRuszkowski, M. / Sikorski, M. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold.
Authors: Ruszkowski, M. / Sliwiak, J. / Ciesielska, A. / Barciszewski, J. / Sikorski, M. / Jaskolski, M.
#1: Journal: Plant Cell / Year: 2006
Title: Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin.
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine.
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The landscape of cytokinin binding by a plant nodulin.
Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
#4: Journal: J.Mol.Biol. / Year: 2008
Title: Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.
Authors: Fernandes, H. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
#5: Journal: Febs J. / Year: 2013
Title: Structural and functional aspects of PR-10 proteins.
Authors: Fernandes, H. / Michalska, K. / Sikorski, M. / Jaskolski, M.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9592
Polymers17,6131
Non-polymers3461
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.380, 54.290, 71.090
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cytokinin-specific binding protein


Mass: 17612.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: vrphbp / Plasmid: PET 3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9ZWP8, UniProt: A0A1S3THR8*PLUS
#2: Chemical ChemComp-GA3 / GIBBERELLIN A3 / (1S,2S,4aR,4bR,7S,9aS,10S,10aR)-2,7-dihydroxy-1-methyl-8-methylidene-13-oxo-1,2,4b,5,6,7,8,9,10,10a-decahydro-4a,1-(epo xymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid


Mass: 346.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22O6 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.86 Å3/Da / Density % sol: 33.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M MMT buffer pH 4.0, 25% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97551 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2013 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97551 Å / Relative weight: 1
ReflectionResolution: 1.42→35.14 Å / Num. all: 24476 / Num. obs: 24350 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 18.06 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.42-1.460.521.98199.3
1.46-1.50.4212.48199.7
1.5-1.540.3752.89199.3
1.54-1.590.3053.77199.6
1.59-1.640.274.32199.5
1.64-1.70.2515.11199.4
1.7-1.760.26.48199.3
1.76-1.830.1857.57199.6
1.83-1.910.1439.15199.6
1.91-2.010.12711.18199.6
2.01-2.120.11512.75198.7
2.12-2.250.10514.43199.3
2.25-2.40.09415.54199.6
2.4-2.590.09516.24199.4
2.59-2.840.08616.95199.6
2.84-3.180.08117.81199.5
3.18-3.670.0718.87199.7
3.67-4.490.06119.21199.8
4.49-6.350.05218.981100
6.35-35.140.04320.51199.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FLH

2flh


Resolution: 1.42→35.14 Å / SU ML: 0.18 / Phase error: 25.01 / Stereochemistry target values: ENGH & HUBER
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflection
Rfree0.2039 1023 4.2 %
Rwork0.152 --
obs0.1543 24350 99.5 %
all-24476 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.53 Å2
Refinement stepCycle: LAST / Resolution: 1.42→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 25 140 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191325
X-RAY DIFFRACTIONf_angle_d1.9111815
X-RAY DIFFRACTIONf_dihedral_angle_d14.854495
X-RAY DIFFRACTIONf_chiral_restr0.125213
X-RAY DIFFRACTIONf_plane_restr0.009226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.49490.32061450.23343316X-RAY DIFFRACTION100
1.4949-1.58850.29991450.20733302X-RAY DIFFRACTION99
1.5885-1.71120.28431460.19623338X-RAY DIFFRACTION99
1.7112-1.88340.23591460.17853319X-RAY DIFFRACTION99
1.8834-2.15590.2381450.15593320X-RAY DIFFRACTION99
2.1559-2.7160.22311460.15293328X-RAY DIFFRACTION99
2.716-35.140.15351500.12773404X-RAY DIFFRACTION100

+
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://pdbjlvh1.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