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- PDB-2qim: Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from... -

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Basic information

Entry
Database: PDB / ID: 2qim
TitleCrystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin
ComponentsPR10.2B
KeywordsALLERGEN / trans-zeatin / cytokinin / plant hormones / plant protein / PR-10 protein / pathogenesis-related protein
Function / homology
Function and homology information


cytokinin binding / response to biotic stimulus / 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 ...cytokinin binding / response to biotic stimulus / 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 / 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
(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: 1.35 Å
AuthorsFernandes, H.C. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / 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.
#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: 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.
#4: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy
Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / Joost van Neerven, R.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
#5: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier.
Authors: Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PR10.2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9157
Polymers16,9061
Non-polymers1,0096
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.822, 73.822, 67.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 16906.000 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) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q9LLQ2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN / Zeatin


Mass: 219.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.2 M sodium citrate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 23, 2005 / Details: mirrors
RadiationMonochromator: Si[111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.35→15 Å / Num. all: 45685 / Num. obs: 45644 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 56.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LlPR-10.2F

Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.642 / SU ML: 0.03
Isotropic thermal model: Anisotropic displacement parameters for non-H atoms
Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19438 1163 2.5 %RANDOM
Rwork0.14725 ---
obs0.14843 44481 99.99 %-
all-45685 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 71 233 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0241304
X-RAY DIFFRACTIONr_bond_other_d0.0010.02825
X-RAY DIFFRACTIONr_angle_refined_deg2.0432.3321761
X-RAY DIFFRACTIONr_angle_other_deg0.9632052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15526.73152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.408151
X-RAY DIFFRACTIONr_chiral_restr0.1120.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2150.2257
X-RAY DIFFRACTIONr_nbd_other0.190.2783
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2643
X-RAY DIFFRACTIONr_nbtor_other0.0890.2696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0531.5801
X-RAY DIFFRACTIONr_mcbond_other3.8931.5325
X-RAY DIFFRACTIONr_mcangle_it6.03121264
X-RAY DIFFRACTIONr_scbond_it9.1673588
X-RAY DIFFRACTIONr_scangle_it11.7024.5497
X-RAY DIFFRACTIONr_rigid_bond_restr4.47732328
X-RAY DIFFRACTIONr_sphericity_free24.1693234
X-RAY DIFFRACTIONr_sphericity_bonded11.3932106
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 84 -
Rwork0.216 3271 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 63.4287 Å / Origin y: 48.9393 Å / Origin z: 0.2718 Å
111213212223313233
T0.0262 Å2-0.0005 Å2-0.0049 Å2-0.0238 Å20.0031 Å2--0.0191 Å2
L0.0783 °20.0484 °20.0043 °2-0.132 °2-0.0309 °2--0.0949 °2
S0.0026 Å °-0.0006 Å °0.0112 Å °-0.0133 Å °0.0074 Å °0.025 Å °0.0054 Å °0.0069 Å °-0.01 Å °

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