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- PDB-8ohw: Crystal structure of heparanase from Burkholderia pseudomallei in... -

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Basic information

Entry
Database: PDB / ID: 8ohw
TitleCrystal structure of heparanase from Burkholderia pseudomallei in complex with siastatin B derived inhibitor
ComponentsGlycoside hydrolase family 44 domain-containing protein
KeywordsHYDROLASE / Inhibitor / Complex
Function / homology: / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Chem-VON / Uncharacterized protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsArmstrong, Z. / Yurong, C. / Wu, L. / Overkleeft, H.S. / Davies, G.J.
Funding support Netherlands, European Union, United Kingdom, 6items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VI.Veni.212.173 Netherlands
European Research Council (ERC)ERC-2011-AdG-290836European Union
European Research Council (ERC)ERC-2012-AdG-32294European Union
European Research Council (ERC)ERC-2020-SyG-951231European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B.
Authors: Chen, Y. / van den Nieuwendijk, A.M.C.H. / Wu, L. / Moran, E. / Skoulikopoulou, F. / van Riet, V. / Overkleeft, H.S. / Davies, G.J. / Armstrong, Z.
History
DepositionMar 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
AAA: Glycoside hydrolase family 44 domain-containing protein
BBB: Glycoside hydrolase family 44 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,12812
Polymers89,2772
Non-polymers85110
Water17,421967
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint9 kcal/mol
Surface area29970 Å2
Unit cell
Length a, b, c (Å)76.370, 104.610, 113.710
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 Glycoside hydrolase family 44 domain-containing protein


Mass: 44638.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSL2070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63T97
#2: Chemical ChemComp-VON / (3~{S},4~{S},5~{S},6~{R})-4,5,6-tris(oxidanyl)piperidine-3-carboxylic acid


Mass: 177.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.27→61.758 Å / Num. obs: 238876 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.999 / Net I/σ(I): 12.6
Reflection shellResolution: 1.27→1.29 Å / Num. unique obs: 11543 / CC1/2: 0.518

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→61.758 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.161 / SU B: 0.776 / SU ML: 0.032 / Average fsc free: 0.9205 / Average fsc work: 0.9237 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1815 12173 5.098 %
Rwork0.1603 226593 -
all0.161 --
obs-238766 99.87 %
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: 17.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.358 Å20 Å20 Å2
2--0.171 Å2-0 Å2
3----0.529 Å2
Refinement stepCycle: LAST / Resolution: 1.27→61.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 56 967 7299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0136654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176010
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.6369110
X-RAY DIFFRACTIONr_angle_other_deg1.6181.56813872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64821.812298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34115875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5551539
X-RAY DIFFRACTIONr_chiral_restr0.1020.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027878
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021443
X-RAY DIFFRACTIONr_nbd_refined0.2230.21364
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.25556
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23312
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2680
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.213
X-RAY DIFFRACTIONr_nbd_other0.2340.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.234
X-RAY DIFFRACTIONr_mcbond_it1.6561.7023596
X-RAY DIFFRACTIONr_mcbond_other1.6341.73595
X-RAY DIFFRACTIONr_mcangle_it2.3992.5494523
X-RAY DIFFRACTIONr_mcangle_other2.4082.554524
X-RAY DIFFRACTIONr_scbond_it2.8151.9283058
X-RAY DIFFRACTIONr_scbond_other2.8141.9283059
X-RAY DIFFRACTIONr_scangle_it4.1122.7984587
X-RAY DIFFRACTIONr_scangle_other4.1112.7994588
X-RAY DIFFRACTIONr_lrange_it5.71522.2767752
X-RAY DIFFRACTIONr_lrange_other5.47721.2787457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.3030.2988680.29216422X-RAY DIFFRACTION98.7718
1.303-1.3390.2798170.27216235X-RAY DIFFRACTION99.7543
1.339-1.3770.2748300.24515800X-RAY DIFFRACTION99.9099
1.377-1.420.2437980.22715355X-RAY DIFFRACTION100
1.42-1.4660.248070.21314855X-RAY DIFFRACTION99.9809
1.466-1.5180.2027560.18814413X-RAY DIFFRACTION99.9802
1.518-1.5750.1887260.17213944X-RAY DIFFRACTION99.9796
1.575-1.6390.1916630.16513442X-RAY DIFFRACTION99.9858
1.639-1.7120.186860.15612868X-RAY DIFFRACTION99.9852
1.712-1.7960.1926970.15312268X-RAY DIFFRACTION99.9923
1.796-1.8930.186490.1511689X-RAY DIFFRACTION99.9838
1.893-2.0080.1656170.14911085X-RAY DIFFRACTION100
2.008-2.1460.1685930.14810398X-RAY DIFFRACTION99.9818
2.146-2.3180.175000.1419790X-RAY DIFFRACTION99.9903
2.318-2.540.1674840.1398989X-RAY DIFFRACTION100
2.54-2.8390.1634910.1378092X-RAY DIFFRACTION99.9651
2.839-3.2780.1654020.1457209X-RAY DIFFRACTION99.9475
3.278-4.0140.1663230.156190X-RAY DIFFRACTION100
4.014-5.6730.1663030.1444781X-RAY DIFFRACTION100
5.673-61.7580.1961630.1852768X-RAY DIFFRACTION99.5922

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