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- PDB-5mxw: Crystal structure of yellow lupin LLPR-10.2B protein in complex w... -

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Basic information

Entry
Database: PDB / ID: 5mxw
TitleCrystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.
ComponentsClass 10 plant pathogenesis-related protein
KeywordsPLANT PROTEIN / phytohormon binding protein / PR-10 protein / melatonin
Function / homology
Function and homology information


cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding ...cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding / nucleus / cytosol
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
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Unknown ligand / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / Class 10 plant pathogenesis-related protein 2B
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsSliwiak, J. / Sikorski, M. / Jaskolski, M.
Funding support2items
OrganizationGrant numberCountry
European UnionFP7/2007-2013
BioStruct-X283570
Citation
Journal: FEBS J. / Year: 2018
Title: PR-10 proteins as potential mediators of melatonin-cytokinin cross-talk in plants: crystallographic studies of LlPR-10.2B isoform from yellow lupine.
Authors: Sliwiak, J. / Sikorski, M. / Jaskolski, M.
#1: Journal: Front Plant Sci / Year: 2016
Title: Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.
Authors: Sliwiak, J. / Dauter, Z. / Jaskolski, M.
#2: Journal: J. Struct. Biol. / Year: 2016
Title: Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein.
Authors: Sliwiak, J. / Dolot, R. / Michalska, K. / Szpotkowski, K. / Bujacz, G. / Sikorski, M. / Jaskolski, M.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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.
#4: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.
Authors: Sliwiak, J. / Dauter, Z. / Kowiel, M. / McCoy, A.J. / Read, R.J. / Jaskolski, M.
#5: Journal: FEBS J. / Year: 2009
Title: Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein.
Authors: Fernandes, H. / Bujacz, A. / Bujacz, G. / Jelen, F. / Jasinski, M. / Kachlicki, P. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#6: 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.
#7: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass.
Authors: Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#8: 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.
#9: 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.
#10: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: The landscape of cytokinin binding by a plant nodulin.
Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 1, 2018Group: Data collection / Derived calculations / Other / Category: pdbx_struct_oper_list / symmetry
Item: _pdbx_struct_oper_list.symmetry_operation / _symmetry.space_group_name_H-M
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class 10 plant pathogenesis-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,13520
Polymers16,6611
Non-polymers47519
Water2,666148
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-12 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.400, 74.400, 67.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Class 10 plant pathogenesis-related protein / PR10.2B


Mass: 16660.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: pr10.2b, Ypr10.2b / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LLQ2

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Non-polymers , 5 types, 167 molecules

#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 16 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ML1 / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Melatonin


Mass: 232.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O2
#5: Chemical ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN


Mass: 219.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.24 Å3/Da / Density % sol: 62.05 % / Description: prism
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 1.4 M sodium citrate pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→46.59 Å / Num. obs: 29524 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.984 % / Biso Wilson estimate: 31.574 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.041 / Χ2: 0.941 / Net I/σ(I): 22.2 / Num. measured all: 147160
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.57-1.664.8920.7442.0122935476446880.7890.83498.4
1.66-1.784.9840.4233.5122355448644850.9280.473100
1.78-1.925.0170.1927.4720954417841770.9820.215100
1.92-2.115.0420.08316.6119304382938290.9960.092100
2.11-2.355.0550.05225.8717592348034800.9980.058100
2.35-2.725.0630.03735.8415619308730850.9990.04199.9
2.72-3.325.010.02650.9813075261026100.9990.029100
3.32-4.694.9280.02163.5710044204320380.9990.02399.8
4.69-46.594.6660.02263.865282114411320.9990.02599

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qim

2qim


Resolution: 1.57→46.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.191 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1057 3.6 %RANDOM
Rwork0.185 ---
obs0.1858 28468 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.5 Å2 / Biso mean: 32.201 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.91 Å2-0 Å2
2---0.91 Å2-0 Å2
3---2.96 Å2
Refinement stepCycle: final / Resolution: 1.57→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 50 149 1361
Biso mean--37.19 38.52 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191248
X-RAY DIFFRACTIONr_bond_other_d0.0020.021201
X-RAY DIFFRACTIONr_angle_refined_deg1.8662.0031688
X-RAY DIFFRACTIONr_angle_other_deg0.7913.0042784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58326.45848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50815214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.424151
X-RAY DIFFRACTIONr_chiral_restr0.120.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021411
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02251
LS refinement shellResolution: 1.57→1.611 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 79 -
Rwork0.321 2019 -
all-2098 -
obs--96.64 %
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)
12.6175-2.98631.24219.0103-3.01552.2127-0.0141-0.3564-0.33040.51380.30230.712-0.29870.0752-0.28810.14860.04620.08070.16710.07450.0861111.56896.8036.976
21.24990.16320.53410.6749-0.11540.6877-0.07720.0426-0.2468-0.10880.1277-0.0723-0.00090.0456-0.05050.0928-0.0090.00840.11750.01110.0934114.87791.168-8.316
32.029-0.05732.07991.3503-1.21063.2073-0.1866-0.0197-0.1085-0.02040.28760.0168-0.1814-0.1401-0.1010.130.0078-0.00320.21840.02230.0103115.26499.555-6.215
41.696-2.8860.1957.426-2.26141.51090.0811-0.0991-0.19180.3936-0.05060.3547-0.37870.1933-0.03060.19320.0240.0210.17170.04960.0336112.353103.4731.652
52.0408-1.9235-0.026810.3487-0.79090.3187-0.0924-0.5317-0.19020.20260.03-0.0929-0.11830.02480.06240.08890.0066-0.00770.21520.03620.0506104.83991.8150.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 76
3X-RAY DIFFRACTION3A77 - 90
4X-RAY DIFFRACTION4A91 - 126
5X-RAY DIFFRACTION5A127 - 155

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