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- PDB-5e97: Glycoside Hydrolase ligand structure 1 -

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Basic information

Entry
Database: PDB / ID: 5e97
TitleGlycoside Hydrolase ligand structure 1
Components(Heparanase) x 2
KeywordsHYDROLASE / glycoside hydrolase / ligand 1 / protein / sugar / hydrolase
Function / homologyNeutrophil degranulation / HS-GAG degradation / Glycosyl hydrolase family 79, N-terminal domain / Glycoside hydrolase superfamily / Glycoside hydrolase, family 79 / heparanase / heparanase activity / vascular wound healing / heparan sulfate proteoglycan catabolic process / regulation of hair follicle development ...Neutrophil degranulation / HS-GAG degradation / Glycosyl hydrolase family 79, N-terminal domain / Glycoside hydrolase superfamily / Glycoside hydrolase, family 79 / heparanase / heparanase activity / vascular wound healing / heparan sulfate proteoglycan catabolic process / regulation of hair follicle development / syndecan binding / beta-glucuronidase activity / positive regulation of hair follicle development / glycosaminoglycan catabolic process / proteoglycan metabolic process / angiogenesis involved in wound healing / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / cell-matrix adhesion / positive regulation of blood coagulation / lysosomal lumen / extracellular matrix / lysosomal membrane / specific granule lumen / lysosome / protein dimerization activity / membrane raft / positive regulation of protein kinase B signaling / intracellular membrane-bounded organelle / neutrophil degranulation / nucleoplasm / extracellular region / nucleus / Heparanase
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.63 Å resolution
AuthorsWu, L. / Davies, G.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural characterization of human heparanase reveals insights into substrate recognition.
Authors: Wu, L. / Viola, C.M. / Brzozowski, A.M. / Davies, G.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 14, 2015 / Release: Nov 18, 2015
RevisionDateData content typeGroupProviderType
1.0Nov 18, 2015Structure modelrepositoryInitial release
1.1Dec 2, 2015Structure modelDatabase references
1.2Dec 16, 2015Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heparanase
B: Heparanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,27315
Polyers52,2762
Non-polymers1,99613
Water7,152397
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11650
ΔGint (kcal/M)-61
Surface area (Å2)18760
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)45.880, 70.890, 78.230
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 2 types, 2 molecules AB

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


Mass: 43733.324 Da / Num. of mol.: 1 / Fragment: residues 158-543 / 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/peptide Heparanase / / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 8542.769 Da / Num. of mol.: 1 / Fragment: residues 36-109 / 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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Non-polymers , 6 types, 410 molecules

#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Formula: Cl / Chloride
#5: Chemical ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6
#6: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#7: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Formula: C6H5NO3 / 4-Nitrophenol
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 / Density percent sol: 47 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: DIAMOND BEAMLINE I04 / Synchrotron site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Collection date: Aug 6, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionD resolution high: 1.63 Å / D resolution low: 38.42 Å / Number obs: 61989 / NetI over sigmaI: 11.7 / Redundancy: 4 % / Percent possible obs: 99.5
Reflection shellRmerge I obs: 0.61 / Highest resolution: 1.64 Å / Lowest resolution: 1.67 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e8m
Correlation coeff Fo to Fc: 0.973 / Correlation coeff Fo to Fc free: 0.961 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 2.156 / Overall SU ML: 0.07 / R Free selection details: taken from apo structure / Cross valid method: THROUGHOUT / Overall ESU R: 0.088 / Overall ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 29.499 Å2 / Aniso B11: 1.02 Å2 / Aniso B12: - Å2 / Aniso B13: 0.57 Å2 / Aniso B22: -0.28 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.82 Å2
Least-squares processR factor R free: 0.19677 / R factor R work: 0.16571 / R factor obs: 0.16733 / Highest resolution: 1.63 Å / Lowest resolution: 38.42 Å / Number reflection R free: 3125 / Number reflection obs: 57972 / Percent reflection R free: 5.1 / Percent reflection obs: 99.79
Refine hist #1Highest resolution: 1.63 Å / Lowest resolution: 38.42 Å
Number of atoms included #1Protein: 3643 / Nucleic acid: 0 / Ligand: 122 / Solvent: 397 / Total: 4162
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193868
X-RAY DIFFRACTIONr_bond_other_d0.0020.0203707
X-RAY DIFFRACTIONr_angle_refined_deg1.6712.0095247
X-RAY DIFFRACTIONr_angle_other_deg0.9743.0008550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365.000459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29023.500160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52415.000649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46915.00022
X-RAY DIFFRACTIONr_chiral_restr0.0970.200599
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.020885
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_it2.1852.6001839
X-RAY DIFFRACTIONr_mcbond_other2.1852.5971838
X-RAY DIFFRACTIONr_mcangle_it3.3283.8852297
X-RAY DIFFRACTIONr_mcangle_other3.3273.8882298
X-RAY DIFFRACTIONr_scbond_it2.9053.0872029
X-RAY DIFFRACTIONr_scbond_other2.9043.0902030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5534.4722951
X-RAY DIFFRACTIONr_long_range_B_refined6.63822.5404619
X-RAY DIFFRACTIONr_long_range_B_other6.63722.5514620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS shellHighest resolution: 1.64 Å / R factor R free: 0.338 / R factor R work: 0.298 / Lowest resolution: 1.683 Å / Number reflection R free: 226 / Number reflection R work: 4264 / Total number of bins used: 20 / Percent reflection obs: 99.82

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