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- PDB-4wp4: Hev b 6.02 (hevein) extracted from surgical gloves -

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Basic information

Entry
Database: PDB / ID: 4wp4
TitleHev b 6.02 (hevein) extracted from surgical gloves
ComponentsPro-hevein
KeywordsALLERGEN / Hevea / lectin / rubber / surgical gloves
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
THIOUREA / Pro-hevein
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.43 Å
AuthorsGalicia, C. / Rodriguez-Romero, A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
DGAPA-UNAMIN207613 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)166472 Mexico
CitationJournal: Mol.Immunol. / Year: 2015
Title: Impact of the vulcanization process on the structural characteristics and IgE recognition of two allergens, Hev b 2 and Hev b 6.02, extracted from latex surgical gloves.
Authors: Galicia, C. / Mendoza-Hernandez, G. / Rodriguez-Romero, A.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pro-hevein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8072
Polymers4,7311
Non-polymers761
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.330, 37.330, 48.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide Pro-hevein / Major hevein


Mass: 4731.166 Da / Num. of mol.: 1 / Fragment: unp residues 18-60 / Source method: isolated from a natural source
Details: Protein purified from rubber surgical gloves that underwent a vulcanization process.
Source: (natural) Hevea brasiliensis (rubber tree) / Plasmid details: Latex from laticiferous cells / References: UniProt: P02877
#2: Chemical ChemComp-TOU / THIOUREA


Mass: 76.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.9 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M sodium citrate, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.43→26.95 Å / Num. obs: 13802 / % possible obs: 99 % / Redundancy: 11.8 % / Biso Wilson estimate: 15.29 Å2
Details: The data collection was done at the maximum crystal-to-detector distance of 72 mm. At this distance the resolution was 1.43 with an I/sigma = 24.4 indicating that the crystal could have ...Details: The data collection was done at the maximum crystal-to-detector distance of 72 mm. At this distance the resolution was 1.43 with an I/sigma = 24.4 indicating that the crystal could have diffracted to a higher resolution. However, this was not possible with our MicroMax007 (Rigaku).
Rmerge(I) obs: 0.058 / Net I/σ(I): 64.6
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 24.4 / % possible all: 96.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1810) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.43→26.947 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.82 / Stereochemistry target values: MLHL
Details: Data collection was done at the maximum crystal-to-detector distance of 72 mm. At this distance the resolution was 1.43 with an I/sigma = 24.4 indicating that the crystal could have ...Details: Data collection was done at the maximum crystal-to-detector distance of 72 mm. At this distance the resolution was 1.43 with an I/sigma = 24.4 indicating that the crystal could have diffracted to a higher resolution. However, this was not possible with our MicroMax007 (Rigaku)
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 -9.88 %Random selection
Rwork0.1515 ---
obs0.1529 6719 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.9 Å2
Refinement stepCycle: LAST / Resolution: 1.43→26.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms321 0 4 53 378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014344
X-RAY DIFFRACTIONf_angle_d1.457467
X-RAY DIFFRACTIONf_dihedral_angle_d16.9129
X-RAY DIFFRACTIONf_chiral_restr0.05642
X-RAY DIFFRACTIONf_plane_restr0.00765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
1.434-1.5440.1561430.14127214.8196.9
1.544-1.70.1621440.131132315.8897.9
1.7-1.9460.1611460.133132213.7199.1
1.946-2.4510.1651520.155137119.5399.8
2.451-26.9520.17081530.1604144015.4599.9
Refinement TLS params.Method: refined / Details: Chain A / Origin x: 12.5351 Å / Origin y: 10.4764 Å / Origin z: 11.9358 Å
111213212223313233
T0.1346 Å20.0128 Å2-0.0013 Å2-0.1059 Å2-0.0029 Å2--0.1381 Å2
L2.7807 °2-1.0731 °20.3882 °2-2.3024 °2-0.2634 °2--2.9011 °2
S-0.0516 Å °-0.0593 Å °0.0511 Å °0.0881 Å °0.0113 Å °0.137 Å °-0.075 Å °-0.1904 Å °0.0423 Å °
Refinement TLS groupSelection: all / Selection details: all

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