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- PDB-7rg8: Crystal Structure of a Stable Heparanase Mutant -

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Basic information

Entry
Database: PDB / ID: 7rg8
TitleCrystal Structure of a Stable Heparanase Mutant
Components
  • Heparanase 50 kDa subunit
  • Heparanase 8 kDa subunit
KeywordsHYDROLASE / Heparanase / Heparan Sulfate
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process ...heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process / vascular wound healing / protein transmembrane transport / establishment of endothelial barrier / angiogenesis involved in wound healing / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / extracellular matrix / lysosomal lumen / cell-matrix adhesion / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / response to antibiotic / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWhitefield, C. / Hong, N.S. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP160101552 Australia
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Computational design and experimental characterisation of a stable human heparanase variant.
Authors: Whitefield, C. / Hong, N. / Mitchell, J.A. / Jackson, C.J.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparanase 50 kDa subunit
B: Heparanase 8 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7947
Polymers53,6432
Non-polymers1515
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-94 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.785, 76.094, 124.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heparanase 50 kDa subunit


Mass: 43375.863 Da / Num. of mol.: 1
Mutation: N178K, A195S, L197G, S212A, S219D, L230R, D234G, E244K, Q248H, R273G, S292A, R307L, I318T, S322Q, F327L, L354G, S426Q, K427D, K477Q, L483H, H486D, L498Q, M512K, E513P, S530A, A540P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251
#2: Protein Heparanase 8 kDa subunit


Mass: 10267.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium Sulfate, Sodium Acetate pH 5.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→53.89 Å / Num. obs: 139784 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 14.9 / Num. measured all: 1829452 / Scaling rejects: 2486
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.3210.71.3177219867750.8510.4211.3851.399.2
7.12-53.8911.10.061110329940.980.0210.06437.499.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E8M

5e8m


Resolution: 1.3→47.01 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.165 6940 4.97 %
Rwork0.1428 132577 -
obs0.1439 139517 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.48 Å2 / Biso mean: 28.6605 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 1.3→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 11 363 4003
Biso mean--23.14 41.23 -
Num. residues----459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.310.26152240.25734350457499
1.31-1.330.26722110.22294294450598
1.33-1.350.2222100.198743674577100
1.35-1.360.23522440.189543914635100
1.36-1.380.20722070.172643584565100
1.38-1.40.22112180.166543944612100
1.4-1.420.21132290.161543964625100
1.42-1.440.17152660.153442884554100
1.44-1.460.19112490.159843884637100
1.46-1.490.22432120.159844154627100
1.49-1.510.18052120.144243834595100
1.51-1.540.16932060.136344124618100
1.54-1.570.16212180.124144204638100
1.57-1.60.14622720.114243104582100
1.6-1.640.14452500.111944214671100
1.64-1.680.14342250.11343874612100
1.68-1.720.14422150.113644214636100
1.72-1.760.13252230.12344224645100
1.76-1.820.16352350.126144514686100
1.82-1.870.16352370.133443614598100
1.87-1.940.15512410.13244424683100
1.94-2.020.13442330.127744134646100
2.02-2.110.15112140.132444514665100
2.11-2.220.13122310.129444724703100
2.22-2.360.14312440.130944504694100
2.36-2.540.16762380.137644484686100
2.54-2.80.17432460.143144674713100
2.8-3.210.16962340.152245174751100
3.21-4.040.16482480.142845654813100
4.04-47.010.17582480.157647234971100

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