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- PDB-1fcq: CRYSTAL STRUCTURE (MONOCLINIC) OF BEE VENOM HYALURONIDASE -

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Basic information

Entry
Database: PDB / ID: 1fcq
TitleCRYSTAL STRUCTURE (MONOCLINIC) OF BEE VENOM HYALURONIDASE
ComponentsHYALURONOGLUCOSAMINIDASE
KeywordsHYDROLASE / 7-stranded (beta/alpha) TIM barrel / glycosidase family 56 / allergen
Function / homology
Function and homology information


hyaluronoglucosaminidase / hyalurononglucosaminidase activity / hyaluronan catabolic process / defense response / carbohydrate metabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 56, bee venom hyaluronidase / Hyaluronidase / Hyaluronidase / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMarkovic-Housley, Z. / Miglierini, G. / Soldatova, L. / Mueller, U. / Schirmer, T.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of hyaluronidase, a major allergen of bee venom.
Authors: Markovic-Housley, Z. / Miglierini, G. / Soldatova, L. / Rizkallah, P.J. / Muller, U. / Schirmer, T.
History
DepositionJul 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYALURONOGLUCOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)40,9011
Polymers40,9011
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.886, 90.229, 49.060
Angle α, β, γ (deg.)90.00, 92.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYALURONOGLUCOSAMINIDASE / HYALURONIDASE / API M II


Mass: 40901.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Cell (production host): HIGH-FIVE INSECT CELLS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08169, hyaluronoglucosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 6000, NaCl, acetic acid, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMsodium acetate1drop
28-10 mg/mlprotein1drop
310 %PEG60001reservoir
41.0 M1reservoirNaCl
520 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 43930 / Num. obs: 43930 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.251 / % possible all: 88
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 88 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 1.6→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 4383 RANDOM
Rwork0.185 --
all0.192 43540 -
obs0.192 43540 -
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 0 354 2963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.022
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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