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- PDB-3e85: Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from... -

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Basic information

Entry
Database: PDB / ID: 3.0E+85
TitleCrystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea
ComponentsPR10.2B
KeywordsPLANT PROTEIN / PLANT HORMONES / CYTOKININ / DIPHENYLUREA / PLANT PR-10 PROTEIN / YELLOW LUPINE / Pathogenesis-related protein / Plant defense
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
1,3-DIPHENYLUREA / Class 10 plant pathogenesis-related protein 2B
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFernandes, H.C. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
Citation
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.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: Journal: Nat.Struct.Mol.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.
#6: 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: Markovi-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H.
History
DepositionAug 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: citation_author / database_2 ...citation_author / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR10.2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8017
Polymers16,9061
Non-polymers8956
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.362, 73.256, 99.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

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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-BSU / 1,3-DIPHENYLUREA / DIPHENYLCARBAMIDE / 1,3-Diphenylurea


Mass: 212.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12N2O / Comment: hormone*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 33.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.4 M Sodium citrate, 0.1 M citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 16, 2005 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 9529 / % possible obs: 99.56 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.8 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QIM

2qim


Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.931 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.198 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 860 9.1 %RANDOM
Rwork0.18788 ---
obs0.19323 8631 99.54 %-
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: 30.611 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2---1.34 Å20 Å2
3---3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 66 134 1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221257
X-RAY DIFFRACTIONr_bond_other_d0.0010.02833
X-RAY DIFFRACTIONr_angle_refined_deg1.8782.0261692
X-RAY DIFFRACTIONr_angle_other_deg0.94132049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89526.45848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87515210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.89151
X-RAY DIFFRACTIONr_chiral_restr0.1060.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
X-RAY DIFFRACTIONr_nbd_refined0.2440.2277
X-RAY DIFFRACTIONr_nbd_other0.2110.2840
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2620
X-RAY DIFFRACTIONr_nbtor_other0.0960.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.289
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.213
X-RAY DIFFRACTIONr_mcbond_it1.0441.5760
X-RAY DIFFRACTIONr_mcbond_other0.2411.5319
X-RAY DIFFRACTIONr_mcangle_it1.852.51225
X-RAY DIFFRACTIONr_scbond_it4.2295506
X-RAY DIFFRACTIONr_scangle_it6.45610467
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 53 -
Rwork0.213 601 -
obs--96.18 %
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)
13.1419-0.28830.46351.54631.41871.47330.01280.1037-0.102-0.1020.0707-0.23590.05130.0884-0.0835-0.0758-0.00840.0448-0.08070.0452-0.166121.591710.21559.8226
23.661.62561.4314.41781.11942.54810.02860.1313-0.37120.07930.0404-0.09580.19030.0119-0.069-0.13560.02050.0549-0.11340.0093-0.22213.35529.822164.2164
34.52243.90977.641214.51242.164314.68290.5927-0.9092-1.06740.0618-0.5033-1.08830.6686-0.1093-0.08940.1759-0.06870.07010.54620.06280.197616.69018.363364.5678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 862 - 87
2X-RAY DIFFRACTION2AA87 - 15488 - 155
3X-RAY DIFFRACTION3AB - E158 - 161

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