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- PDB-6zdm: Crystal structure of human heparanase in complex with a N',6O'-bi... -

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Basic information

Entry
Database: PDB / ID: 6zdm
TitleCrystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide
Components(Heparanase) x 2
KeywordsHYDROLASE / heparanase / substrate / fluorogenic / heparan sulfate / poised / 4-methylumbelliferyl
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / syndecan binding ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / syndecan binding / protein transmembrane transport / vascular wound healing / angiogenesis involved in wound healing / establishment of endothelial barrier / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / : / lysosomal lumen / extracellular matrix / cell-matrix adhesion / specific granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / membrane raft / lysosomal membrane / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-QG2 / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.714 Å
AuthorsWu, L. / Davies, G.J.
Funding support United Kingdom, Australia, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2012-AdG-322942 United Kingdom
Australian Research Council (ARC)DP170104431 Australia
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Structural insights into heparanase activity using a fluorogenic heparan sulfate disaccharide.
Authors: Wu, L. / Wimmer, N. / Davies, G.J. / Ferro, V.
History
DepositionJun 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Heparanase
BBB: Heparanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71310
Polymers52,2762
Non-polymers1,4378
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, both chains elute as one peak by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-121 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.974, 70.856, 78.455
Angle α, β, γ (deg.)90.000, 97.128, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AAABBB

#1: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 43733.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKAD IFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPD ...Details: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKAD IFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPD VLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLV DENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQ VDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase
#2: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 8542.769 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase

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Sugars , 1 types, 1 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 198 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-QG2 / (2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 673.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27NO19S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.68→52.4 Å / Num. obs: 24849 / % possible obs: 91 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.025 / Net I/σ(I): 7.8
Reflection shellResolution: 1.68→1.951 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1243 / CC1/2: 0.692 / Rpim(I) all: 0.371 / % possible all: 65.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
STARANISOdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e8m

5e8m


Resolution: 1.714→52.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.36 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.282 / ESU R Free: 0.22
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2412 1206 4.857 %
Rwork0.1788 23624 -
all0.182 --
obs-24830 47.266 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.282 Å2
2---0.527 Å2-0 Å2
3---0.267 Å2
Refinement stepCycle: LAST / Resolution: 1.714→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 87 191 3906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133828
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173582
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6645201
X-RAY DIFFRACTIONr_angle_other_deg1.2051.598312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82821.868182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99915647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2271522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2090.2793
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23399
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21825
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.213
X-RAY DIFFRACTIONr_nbd_other0.2530.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2970.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1950.21
X-RAY DIFFRACTIONr_mcbond_it3.1074.0271840
X-RAY DIFFRACTIONr_mcbond_other3.1074.0241839
X-RAY DIFFRACTIONr_mcangle_it4.7186.0152300
X-RAY DIFFRACTIONr_mcangle_other4.7176.0192301
X-RAY DIFFRACTIONr_scbond_it3.2754.3921988
X-RAY DIFFRACTIONr_scbond_other3.1744.3711965
X-RAY DIFFRACTIONr_scangle_it5.0856.4262901
X-RAY DIFFRACTIONr_scangle_other4.9796.4042870
X-RAY DIFFRACTIONr_lrange_it7.57347.2824256
X-RAY DIFFRACTIONr_lrange_other7.41647.2274227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
1.714-1.7590.33910.202620.20438790.8941.62410.194
1.759-1.8070.319100.2181670.22437520.8434.71750.220.852
1.807-1.8590.232150.2392940.23837160.8258.31540.2390.774
1.859-1.9170.271150.233760.23235160.84711.12060.2310.799
1.917-1.9790.336210.2255140.22934600.84515.46240.2120.771
1.979-2.0490.254400.2256850.22733400.84321.70660.2170.832
2.049-2.1260.275350.2199280.22132180.85729.92540.2010.837
2.126-2.2130.282660.2112720.21331010.87443.14740.1870.836
2.213-2.3110.289790.21914660.22229810.8751.82820.1990.859
2.311-2.4240.285910.21916240.22228240.87360.72950.1980.816
2.424-2.5550.2951070.21317830.21827160.87669.58760.1890.863
2.555-2.710.2621110.21419640.21725920.88980.0540.1950.878
2.71-2.8960.281080.20520380.20924000.89389.41670.1880.846
2.896-3.1280.2681060.19220960.19622400.91498.30360.1810.889
3.128-3.4260.26910.18719820.1920800.9399.66350.1880.905
3.426-3.830.243860.16818070.17118950.94999.89450.1780.924
3.83-4.420.188820.1515820.15216680.95799.76020.170.956
4.42-5.4090.176590.13913330.14113950.96399.78490.1710.959
5.409-7.6320.26500.17310560.17711130.94399.37110.2160.918
7.632-77.8490.215330.155950.1536300.96599.68250.2430.944

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