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- PDB-7prb: Crystal structure of Burkholderia pseudomallei heparanase in comp... -

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Basic information

Entry
Database: PDB / ID: 7prb
TitleCrystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor GR109
ComponentsGlyco_hydro_44 domain-containing protein
KeywordsHYDROLASE / glycoside hydrolase / carbohydrate / glucuronidase / GH79
Function / homology: / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Uncharacterized protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsWu, L. / Armstrong, Z. / Davies, G.J.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2011-AdG-290836 United Kingdom
European Research Council (ERC)ERC-2012-AdG-322942 United Kingdom
Netherlands Organisation for Scientific Research (NWO) United Kingdom
Israel Science Foundation1021/19 United Kingdom
European Molecular Biology Organization (EMBO)STF8184 United Kingdom
Royal Society United Kingdom
Wellcome Trust218579/Z/19/Z United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo.
Authors: de Boer, C. / Armstrong, Z. / Lit, V.A.J. / Barash, U. / Ruijgrok, G. / Boyango, I. / Weitzenberg, M.M. / Schroder, S.P. / Sarris, A.J.C. / Meeuwenoord, N.J. / Bule, P. / Kayal, Y. / Ilan, N. ...Authors: de Boer, C. / Armstrong, Z. / Lit, V.A.J. / Barash, U. / Ruijgrok, G. / Boyango, I. / Weitzenberg, M.M. / Schroder, S.P. / Sarris, A.J.C. / Meeuwenoord, N.J. / Bule, P. / Kayal, Y. / Ilan, N. / Codee, J.D.C. / Vlodavsky, I. / Overkleeft, H.S. / Davies, G.J. / Wu, L.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 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: Glyco_hydro_44 domain-containing protein
B: Glyco_hydro_44 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,69411
Polymers89,2772
Non-polymers1,4179
Water17,853991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, protein elutes as a single peak at expected position for a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint10 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.210, 101.070, 113.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 10 - 445 / Label seq-ID: 2 - 437

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Glyco_hydro_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 (strain K96243) (bacteria)
Strain: K96243 / Gene: BPSL2070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63T97
#2: Polysaccharide 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl) ...2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid


Type: oligosaccharide / Mass: 491.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,1,0/[a2122h-1a_1-5_1*OC^RC^SC^RC^SC^SC^R$3/8O/7O/6O/5O/4CO/13=O_2*NCC/3=O_6*OSO/3=O/3=O]/1/WURCSPDB2Glycan 1.1.0
[][<C7O5>]{[(1+1)][a-D-GlcpNAc6SO3]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / 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: 1.31→66.06 Å / Num. obs: 220199 / % possible obs: 98.5 % / Redundancy: 8.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 15.7
Reflection shellResolution: 1.31→1.34 Å / Rmerge(I) obs: 1.493 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 15818 / CC1/2: 0.682 / Rpim(I) all: 0.534

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bwi

5bwi


Resolution: 1.31→66.06 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.983 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1855 11043 5.017 %
Rwork0.1657 209063 -
all0.167 --
obs-220106 98.361 %
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: 22.799 Å2
Baniso -1Baniso -2Baniso -3
1-1.858 Å2-0 Å20 Å2
2---0.637 Å2-0 Å2
3----1.221 Å2
Refinement stepCycle: LAST / Resolution: 1.31→66.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 90 991 7372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136749
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176214
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6549257
X-RAY DIFFRACTIONr_angle_other_deg1.6071.58414245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70121.776304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13315888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5681541
X-RAY DIFFRACTIONr_chiral_restr0.2930.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028820
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021605
X-RAY DIFFRACTIONr_nbd_refined0.2330.21316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.25733
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23357
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2739
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.216
X-RAY DIFFRACTIONr_nbd_other0.3260.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2540.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0790.21
X-RAY DIFFRACTIONr_mcbond_it1.8112.2013606
X-RAY DIFFRACTIONr_mcbond_other1.8022.23605
X-RAY DIFFRACTIONr_mcangle_it2.4813.2994539
X-RAY DIFFRACTIONr_mcangle_other2.4843.34540
X-RAY DIFFRACTIONr_scbond_it2.8782.4433143
X-RAY DIFFRACTIONr_scbond_other2.8772.4433144
X-RAY DIFFRACTIONr_scangle_it4.3053.5664718
X-RAY DIFFRACTIONr_scangle_other4.3043.5664719
X-RAY DIFFRACTIONr_lrange_it5.61628.3917778
X-RAY DIFFRACTIONr_lrange_other5.34227.3357449
X-RAY DIFFRACTIONr_ncsr_local_group_10.0860.0513890
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.086410.05008
12BX-RAY DIFFRACTIONLocal ncs0.086410.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.3440.3177890.3115010X-RAY DIFFRACTION96.353
1.344-1.3810.3017790.28314731X-RAY DIFFRACTION96.7561
1.381-1.4210.2697400.26414404X-RAY DIFFRACTION97.339
1.421-1.4650.277200.24414009X-RAY DIFFRACTION97.6271
1.465-1.5130.2337210.21913642X-RAY DIFFRACTION97.8473
1.513-1.5660.2227150.20213194X-RAY DIFFRACTION97.9438
1.566-1.6250.2026430.18112834X-RAY DIFFRACTION98.1645
1.625-1.6910.2116410.17412338X-RAY DIFFRACTION98.4974
1.691-1.7660.1956430.1711862X-RAY DIFFRACTION98.7133
1.766-1.8520.195990.16711422X-RAY DIFFRACTION99.0116
1.852-1.9530.1915890.16410852X-RAY DIFFRACTION99.1937
1.953-2.0710.1895550.16610287X-RAY DIFFRACTION99.1949
2.071-2.2140.1915200.169718X-RAY DIFFRACTION99.3595
2.214-2.3910.1714760.1489118X-RAY DIFFRACTION99.6055
2.391-2.6190.1684460.1428397X-RAY DIFFRACTION99.7856
2.619-2.9280.1684040.1467645X-RAY DIFFRACTION99.9379
2.928-3.3810.1653650.1536765X-RAY DIFFRACTION99.9159
3.381-4.140.1613150.1485729X-RAY DIFFRACTION99.7524
4.14-5.8510.162520.1484526X-RAY DIFFRACTION99.8537
5.851-66.060.2291310.192580X-RAY DIFFRACTION98.546

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