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- PDB-1wkx: Crystal Structure of a Hev b 6.02 Isoallergen -

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Basic information

Entry
Database: PDB / ID: 1wkx
TitleCrystal Structure of a Hev b 6.02 Isoallergen
ComponentsHEVEIN ISOFORM 2
KeywordsALLERGEN / isoform / lectin / agglutinin-toxin motif
Function / homology
Function and homology information


chitin binding / defense response to fungus / RNA nuclease activity / defense response to bacterium
Similarity search - Function
Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein ...Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / RlpA-like domain superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Prohevein / Pro-hevein
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsReyes-Lopez, C.A. / Rodriguez-Romero, A.
CitationJournal: to be published
Title: Structural and Immunological Characterization of an Isoallergen of Hev b 6.02
Authors: Reyes-Lopez, C.A. / Hernandez-Arana, A. / Pedraza-Escalona, M. / Hernandez-Santoyo, A. / Mendoza, G. / Llinas, P. / Orozco-Martinez, S. / Huerta, J. / Rodriguez-Romero, A.
History
DepositionJun 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 25, 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: HEVEIN ISOFORM 2


Theoretical massNumber of molelcules
Total (without water)4,7321
Polymers4,7321
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.20, 37.20, 48.79
Angle α, β, γ (deg.)90.0, 90.0, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-74-

HOH

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Components

#1: Protein/peptide HEVEIN ISOFORM 2 / HEV B 6.02 ISOALLERGEN / HEVEIN ISOLECTIN 2


Mass: 4732.151 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hevea brasiliensis (rubber tree) / Tissue: LATEX / References: UniProt: O49860, UniProt: P02877*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.93 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: MPD, Tris, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 23, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→16.27 Å / Num. all: 4440 / Num. obs: 4440 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 25.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 4.5 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q9B

1q9b


Resolution: 1.7→16.265 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.72 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 465 10.5 %RANDOM
Rwork0.152 ---
all0.156 3975 --
obs0.156 3975 100 %-
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: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.7→16.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms321 0 0 40 361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02332
X-RAY DIFFRACTIONr_bond_other_d0.0010.02241
X-RAY DIFFRACTIONr_angle_refined_deg2.3961.93450
X-RAY DIFFRACTIONr_angle_other_deg1.0883579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.465542
X-RAY DIFFRACTIONr_chiral_restr0.1140.241
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02387
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0260
X-RAY DIFFRACTIONr_nbd_refined0.2190.270
X-RAY DIFFRACTIONr_nbd_other0.2680.2281
X-RAY DIFFRACTIONr_nbtor_other0.0870.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.211
X-RAY DIFFRACTIONr_mcbond_it1.2921.5212
X-RAY DIFFRACTIONr_mcangle_it2.0612332
X-RAY DIFFRACTIONr_scbond_it3.2343120
X-RAY DIFFRACTIONr_scangle_it4.7844.5118
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 36 -
Rwork0.249 262 -
obs-298 100 %
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)
12.0191-0.0799-0.35641.2944-0.34421.489-0.0110.0417-0.0349-0.03710.02670.03250.0241-0.0021-0.01570.0195-0.0017-0.00710.0337-0.00440.01552.998616.321712.8491
21.678-0.24980.74030.7514-0.64191.6953-0.01310.0823-0.056-0.0620.0011-0.03890.06770.07180.0120.00860.00130.00870.0138-0.00580.01253.163216.055211.7065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 83

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