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- PDB-1ifv: CRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1B FROM ... -

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Basic information

Entry
Database: PDB / ID: 1ifv
TitleCRYSTAL STRUCTURE OF PATHOGENESIS-RELATED PROTEIN LLPR10.1B FROM YELLOW LUPINE
ComponentsPROTEIN LLR18B
KeywordsALLERGEN / 7-STRANDED BETA SHEET / C-TERMINAL HELIX
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
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 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 13, 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 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE PROTEIN IS MONOMERIC AND THE TWO CHAINS, A AND B, ARE NOT INVOLVED IN QUATERNARY STRUCTURE FORMATION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN LLR18B
B: PROTEIN LLR18B


Theoretical massNumber of molelcules
Total (without water)33,0912
Polymers33,0912
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.880, 107.445, 46.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN LLR18B / LLPR10.1B


Mass: 16545.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Plasmid: PET3A-LLPR10.1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52779
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.47 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.6 mg/mlprotein11
20.9 Msodium citrate11
30.1 MHEPES11pH8.0

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 9, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 15752 / Num. obs: 15752 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.64 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.26
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.78 / Num. unique all: 1498 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 15594 / Redundancy: 5.6 % / Num. measured all: 88882 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
Lowest resolution: 2.39 Å / % possible obs: 94.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
EPMRphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LlPR10.1A

Resolution: 2.25→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1857189.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE ASYMMETRIC UNIT CONTAINS TWO INDEPENDENT CHAINS, NOT INVOLVED IN QUATERNARY STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1539 9.9 %RANDOM
Rwork0.186 ---
all0.188 15594 --
obs0.188 15594 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.41 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.25→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 112 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it3.722
X-RAY DIFFRACTIONc_scbond_it3.762
X-RAY DIFFRACTIONc_scangle_it5.742.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 226 9.1 %
Rwork0.252 2262 -
obs-2262 94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 12 Å / Rfactor all: 0.188 / Rfactor obs: 0.186 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor Rwork: 0.252

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