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- PDB-1fcv: CRYSTAL STRUCTURE OF BEE VENOM HYALURONIDASE IN COMPLEX WITH HYAL... -

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Basic information

Entry
Database: PDB / ID: 1fcv
TitleCRYSTAL STRUCTURE OF BEE VENOM HYALURONIDASE IN COMPLEX WITH HYALURONIC ACID TETRAMER
ComponentsHYALURONOGLUCOSAMINIDASE
KeywordsHYDROLASE / 7 stranded TIM barrel / allergen / glycosidase family 56 / hyaluronic acid
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 / Resolution: 2.65 Å
AuthorsMarkovic-Housley, Z. / Miglierini, G. / Soldatova, L. / Rizkallah, P.J. / 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: Non-polymer description / Version format compliance
Revision 1.3Nov 25, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _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: HYALURONOGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8542
Polymers40,9011
Non-polymers9531
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.012, 71.012, 151.326
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: Polysaccharide alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 952.772 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAa1-3DGlcpNAcb1-4DGlcpAa1-3DGlcpNAcb1-4DGlcpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122A-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1/a4-b1_b3-c1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulphate, Na acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMsodium acetate1drop
28-10 mg/mlprotein1drop
330 %PEG80001reservoir
40.1 Msodium cacodylate1reservoir
50.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 13411 / Num. obs: 13411 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.295 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.65→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 1295 RANDOM
Rwork0.163 --
all0.18 12837 -
obs0.18 12387 -
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 53 132 2866
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.032
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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