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- PDB-1icx: CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM ... -

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Basic information

Entry
Database: PDB / ID: 1icx
TitleCRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1A FROM YELLOW LUPINE
ComponentsPROTEIN LLR18A
KeywordsALLERGEN / 7-stranded beta sheet / C-terminal helix
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
Pathogenesis-related proteins Bet v I family signature. / 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
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBiesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Structure Determination of Lupinus luteus PR10 Protein
Authors: Biesiadka, J. / Sikorski, M.M. / Bujacz, G. / Jaskolski, M.
#2: Journal: Plant Sci. / Year: 1999
Title: Expression of Genes Encoding PR10 Class Pathogenesis-Related Proteins is Inhibited in Yellow Lupine Root Nodules
Authors: Sikorski, M.M. / Biesiadka, J. / Kasperska, A.E. / Kopcinska, J. / Lotocka, B. / Golinowski, W. / Legocki, A.B.
#3: 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.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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

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Assembly

Deposited unit
A: PROTEIN LLR18A


Theoretical massNumber of molelcules
Total (without water)16,7491
Polymers16,7491
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.973, 56.617, 61.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN LLR18A / LLPR10.1A


Mass: 16748.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Plasmid: PET3A-LLPR10.1A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52778
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, TRIS, sucrose laureate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 17, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 1.95→19.35 Å / Num. obs: 9446 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9.46 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.73
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.46 / % possible all: 96.8
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 9.5 % / Num. measured all: 89375 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Lowest resolution: 2.07 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTV
Resolution: 1.95→12 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: RESIDUES ASP 60, GLN 133, LYS 135, PHE 136 REFINED AS ALANINES BECAUSE OF POOR SIDE-CHAIN ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 930 10 %RANDOM
Rwork0.196 ---
obs0.196 9307 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.41 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 104 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.061.5
X-RAY DIFFRACTIONc_mcangle_it3.32
X-RAY DIFFRACTIONc_scbond_it2.982
X-RAY DIFFRACTIONc_scangle_it4.432.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 172 11.5 %
Rwork0.212 1318 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 12 Å / % reflection Rfree: 10 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / Rfactor Rwork: 0.212

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