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- PDB-2pe4: Structure of Human Hyaluronidase 1, a Hyaluronan Hydrolyzing Enzy... -

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Basic information

Entry
Database: PDB / ID: 2pe4
TitleStructure of Human Hyaluronidase 1, a Hyaluronan Hydrolyzing Enzyme Involved in Tumor Growth and Angiogenesis
ComponentsHyaluronidase-1
KeywordsHYDROLASE / Hyaluronidase / Hyaluronan / EGF-like domain
Function / homology
Function and homology information


hyaluranon cable / MPS IX - Natowicz syndrome / positive regulation of hyaluranon cable assembly / hyaluronan metabolic process / chondroitin sulfate catabolic process / hyaluronoglucosaminidase / hyaluronan synthase activity / embryonic skeletal joint morphogenesis / CS/DS degradation / positive regulation of growth ...hyaluranon cable / MPS IX - Natowicz syndrome / positive regulation of hyaluranon cable assembly / hyaluronan metabolic process / chondroitin sulfate catabolic process / hyaluronoglucosaminidase / hyaluronan synthase activity / embryonic skeletal joint morphogenesis / CS/DS degradation / positive regulation of growth / Hyaluronan uptake and degradation / hyalurononglucosaminidase activity / hyaluronan biosynthetic process / cellular response to pH / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / cartilage development / cellular response to UV-B / cellular response to platelet-derived growth factor stimulus / positive regulation of epithelial cell migration / transcription factor binding / positive regulation of cell adhesion / positive regulation of G1/S transition of mitotic cell cycle / cellular response to interleukin-1 / lysosomal lumen / positive regulation of epithelial cell proliferation / response to reactive oxygen species / response to virus / negative regulation of cell growth / positive regulation of angiogenesis / cellular response to tumor necrosis factor / cytoplasmic vesicle / positive regulation of cell growth / carbohydrate metabolic process / lysosome / inflammatory response / symbiont entry into host cell / response to antibiotic / extracellular space / extracellular exosome / cytoplasm
Similarity search - Function
Hyaluronidase / Hyaluronidase / EGF-like domain signature 2. / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Hyaluronidase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChao, K.L. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of Human Hyaluronidase-1, a Hyaluronan Hydrolyzing Enzyme Involved in Tumor Growth and Angiogenesis
Authors: Chao, K.L. / Muthukumar, L. / Herzberg, O.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Hyaluronidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,41711
Polymers47,4141
Non-polymers2,00310
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.050, 92.050, 143.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hyaluronidase-1 / Hyal-1 / Hyaluronoglucosaminidase-1 / LUCA-1


Mass: 47414.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HYAL1, LUCA1 / Plasmid: pMT/BiP/Hyal1iso1 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 cells / References: UniProt: Q12794, hyaluronoglucosaminidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 343 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.5 M sodium chloride, 10% ethanol, 3% galactose, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2006
RadiationMonochromator: cryogenically cooled double crystal Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30.65 Å / Num. all: 47955 / Num. obs: 47955 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.48 % / Rmerge(I) obs: 0.063 / Χ2: 0.76 / Net I/σ(I): 14 / Scaling rejects: 3800
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.078.720.4883.44086646300.9597.7
2.07-2.1510.420.3714.74953647320.8998.7
2.15-2.2510.460.2955.74943947020.8499.1
2.25-2.3710.530.2157.15028547500.7999.4
2.37-2.5210.580.16295043047400.7599.6
2.52-2.7110.590.12211.35135148250.7199.8
2.71-2.9910.680.08714.95141047970.6699.8
2.99-3.4210.750.06519.95221348370.6399.9
3.42-4.3111.060.05425.55452448900.67100
4.31-30.6510.950.04433.45651650520.7599.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.93 Å
Translation3 Å19.93 Å

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FCU

1fcu


Resolution: 2→30.65 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: TLS refinement with 2 groups
RfactorNum. reflectionSelection details
Rfree0.23 -Random
Rwork0.19 --
all0.19 32231 -
obs0.19 32231 -
Displacement parametersBiso mean: 37.023 Å2
Refinement stepCycle: LAST / Resolution: 2→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 134 335 3753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.823

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