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- PDB-4psb: Crystal Structure of Phytohormone Binding Protein from Vigna radi... -

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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


cytokinin binding / gibberellin 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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