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- PDB-4q0k: Crystal Structure of Phytohormone Binding Protein from Medicago t... -

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Basic information

Entry
Database: PDB / ID: 4q0k
TitleCrystal Structure of Phytohormone Binding Protein from Medicago truncatula in complex with gibberellic acid (GA3)
ComponentsPHYTOHORMONE BINDING PROTEIN MTPHBP
KeywordsHORMONE BINDING PROTEIN / CYTOKININ-SPECIFIC BINDING PROTEIN (CSBP) / PR-10 FOLD / PLANT HORMONE BINDING / GIBBERELLIN
Function / homology
Function and homology information


gibberellic acid mediated signaling pathway / 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/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
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsCiesielska, A. / Barciszewski, J. / Ruszkowski, M. / Jaskolski, M. / Sikorski, 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
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionApr 23, 2014ID: 3US7
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Structure summary
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3Sep 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: PHYTOHORMONE BINDING PROTEIN MTPHBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8277
Polymers18,0201
Non-polymers8076
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 55.800, 99.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PHYTOHORMONE BINDING PROTEIN MTPHBP


Mass: 18020.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: mtphbp, MTR_3g055120 / Plasmid: pet151D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G7J032
#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M ADA, 1.0 M AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 27, 2011
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI -111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.34→34.75 Å / Num. all: 39077 / Num. obs: 38199 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 10.87 % / Biso Wilson estimate: 14.62 Å2 / Rmerge(I) obs: 0.043 / Χ2: 0.954 / Net I/σ(I): 30.64
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.34-1.440.8721.91369296546188.3
1.44-1.540.4984.43502635586199.8
1.54-1.670.2879.336995755971100
1.67-1.830.15317.036154748961100
1.83-2.040.07133.525460943191100
2.04-2.360.04254.135023939611100
2.36-2.890.03270.994204333101100
2.89-4.070.02496.923199525531100
1761314311

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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: 2FLH

2flh


Resolution: 1.34→34.75 Å / SU ML: 0.09 / Phase error: 16.94 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. ANISOTROPIC REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1572 1000 2.62 %RANDOM
Rwork0.1229 ---
all0.1238 38199 --
obs0.1238 38196 97.8 %-
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 21.1523 Å2 / Biso min: 9.75 Å2
Refinement stepCycle: LAST / Resolution: 1.34→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 55 193 1466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191347
X-RAY DIFFRACTIONf_angle_d1.6511841
X-RAY DIFFRACTIONf_chiral_restr0.111218
X-RAY DIFFRACTIONf_plane_restr0.009225
X-RAY DIFFRACTIONf_dihedral_angle_d14.992501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.34-1.420.25611250.20494629475486
1.42-1.50.22041440.14955367551199
1.5-1.620.14491460.104854205566100
1.62-1.780.14141460.096954385584100
1.78-2.040.131460.092154185564100
2.04-2.570.13731460.122454335579100
2.57-34.750.16551470.130754915638100

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