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- PDB-5l9z: Crystal structure of human heparanase nucleophile mutant (E343Q),... -

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Basic information

Entry
Database: PDB / ID: 5l9z
TitleCrystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355
Components(Heparanase) x 2
KeywordsHYDROLASE / Heparanase / Probe / GH79
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / beta-glucuronidase activity / 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 / HS-GAG degradation / beta-glucuronidase activity / 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 / lysosomal lumen / cell-matrix adhesion / extracellular matrix / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / intracellular membrane-bounded organelle / lysosomal membrane / response to antibiotic / 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
Chem-GUX / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsWu, L. / Jin, Y. / Davies, G.J.
Funding support United Kingdom, Netherlands, China, 4items
OrganizationGrant numberCountry
European Research CouncilErC-2012-AdG-322942 United Kingdom
European Research CouncilErC-2011-AdG-290836 Netherlands
Netherlands Organization for Scientific Research Netherlands
China Scholarship Council China
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Activity-based probes for functional interrogation of retaining beta-glucuronidases.
Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / ...Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJun 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 23, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 10, 2024Group: 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
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparanase
B: Heparanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,04317
Polymers52,2752
Non-polymers1,76815
Water7,242402
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-54 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.190, 71.050, 78.690
Angle α, β, γ (deg.)90.00, 95.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 43732.340 Da / Num. of mol.: 1 / Fragment: UNP residues 158-543
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
#2: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 8542.769 Da / Num. of mol.: 1 / Fragment: UNP residues 36-109
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, 4 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.: 4
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, 413 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GUX / (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid


Mass: 342.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 17% PEG3350 0.1 M MES 5.5 0.1 M MgCl2 200 nL:500 nL protein:drop ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.57→46 Å / Num. obs: 70155 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.8
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E8M

5e8m


Resolution: 1.57→46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.881 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19334 3448 4.9 %RANDOM
Rwork0.16593 ---
obs0.1673 66696 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å2-0 Å20.21 Å2
2---1.18 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.57→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 111 402 4156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193923
X-RAY DIFFRACTIONr_bond_other_d0.0020.023785
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9975313
X-RAY DIFFRACTIONr_angle_other_deg1.01638734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06423.62163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25715663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.681522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214357
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02901
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3682.6241884
X-RAY DIFFRACTIONr_mcbond_other2.3642.6211883
X-RAY DIFFRACTIONr_mcangle_it3.6853.9192369
X-RAY DIFFRACTIONr_mcangle_other3.6843.9222370
X-RAY DIFFRACTIONr_scbond_it3.0993.1282039
X-RAY DIFFRACTIONr_scbond_other3.0983.1282039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8364.5082942
X-RAY DIFFRACTIONr_long_range_B_refined7.21133.6764632
X-RAY DIFFRACTIONr_long_range_B_other7.21133.6774633
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 240 -
Rwork0.288 4881 -
obs--98.37 %

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