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- PDB-9gv9: Structure of Heparinase I from Bacteroides eggerthii in complex w... -

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Basic information

Entry
Database: PDB / ID: 9gv9
TitleStructure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor and delta-UA(1-4)Glc 3, 6, N-Sulphated disaccharide
ComponentsHeparin lyase I
KeywordsLYASE / Heparin / Heparan Sulphate / Heparinase / Heparitinase
Function / homologyPolysaccharide lyase / Polysaccharide lyase / Prokaryotic membrane lipoprotein lipid attachment site profile. / lyase activity / ACETATE ION / Heparin lyase I
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.715 Å
AuthorsMycroft-West, C. / Wu, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust218579/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Bacteroides eggerthii heparin lyase I liberates the rare delta-GlcA(alpha1->4)Glc3,6,N-sulphated disaccharide motif contained within the pentasaccharide of the clinical anticoagulant fondaparinux sodium
Authors: Kandola, T.K. / Mycroft-West, C. / Andrade De Lima, M.L. / Turner, A. / Gardini, C. / Urso, E. / Miller, G.J. / Bisio, A. / Yates, E.A. / Guerrini, M. / Wu, L. / Skidmore, M.A.
History
DepositionSep 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Heparin lyase I
A: Heparin lyase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,17927
Polymers87,1492
Non-polymers3,03025
Water10,413578
1
B: Heparin lyase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,10014
Polymers43,5741
Non-polymers1,52613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heparin lyase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,07813
Polymers43,5741
Non-polymers1,50412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.59, 91.563, 73.443
Angle α, β, γ (deg.)90, 95.593, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-703-

HOH

21A-712-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 8 - 374 / Label seq-ID: 8 - 374

Dom-ID
1
2

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

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Heparin lyase I


Mass: 43574.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Gene: HMPREF1016_01920 / Production host: Escherichia coli (E. coli) / References: UniProt: E5WZ15
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D- ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 577.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: delta-UA(1-4)Glc 3, 6, N-Sulphated disaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO33SO36SO3]{[(4+1)][a-L-4-deoxy-IdopA]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 601 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.80088806 Å3/Da / Density % sol: 56.1126366 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 5.0, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953738 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953738 Å / Relative weight: 1
ReflectionResolution: 1.715→76.452 Å / Num. obs: 56421 / % possible obs: 90.4 % / Redundancy: 6.7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7.7
Reflection shellResolution: 1.715→1.896 Å / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2821 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.715→76.452 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.071 / SU ML: 0.118 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2415 2859 5.068 %
Rwork0.2037 53559 -
all0.206 --
obs-56418 57.306 %
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: 19.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å2-0 Å2-0.087 Å2
2--0.019 Å2-0 Å2
3----0.062 Å2
Refinement stepCycle: LAST / Resolution: 1.715→76.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 101 648 6637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126212
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165695
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.8538396
X-RAY DIFFRACTIONr_angle_other_deg0.4171.79713186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.6436.83348
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.08614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.646101061
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.4410281
X-RAY DIFFRACTIONr_chiral_restr0.0580.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021412
X-RAY DIFFRACTIONr_nbd_refined0.1910.21065
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25290
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22917
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23112
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2514
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.221
X-RAY DIFFRACTIONr_nbd_other0.1490.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.237
X-RAY DIFFRACTIONr_mcbond_it0.7861.4192953
X-RAY DIFFRACTIONr_mcbond_other0.7821.4182947
X-RAY DIFFRACTIONr_mcangle_it1.3722.5423672
X-RAY DIFFRACTIONr_mcangle_other1.3722.5433673
X-RAY DIFFRACTIONr_scbond_it0.8441.5733259
X-RAY DIFFRACTIONr_scbond_other0.8311.5453196
X-RAY DIFFRACTIONr_scangle_it1.452.8334724
X-RAY DIFFRACTIONr_scangle_other1.4512.7884635
X-RAY DIFFRACTIONr_lrange_it3.31815.1046958
X-RAY DIFFRACTIONr_lrange_other3.18114.4036834
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.0512193
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.08050.0501
12BX-RAY DIFFRACTIONLocal ncs0.08050.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.715-1.7590.26780.305132X-RAY DIFFRACTION1.9308
1.759-1.8070.322230.29452X-RAY DIFFRACTION6.6845
1.807-1.860.274660.2481054X-RAY DIFFRACTION16.2956
1.86-1.9170.29990.2781676X-RAY DIFFRACTION26.7521
1.917-1.980.249960.262111X-RAY DIFFRACTION34.0062
1.98-2.0490.2521340.2292759X-RAY DIFFRACTION46.0302
2.049-2.1260.2671670.2332911X-RAY DIFFRACTION51.2573
2.126-2.2130.2511890.2163388X-RAY DIFFRACTION60.937
2.213-2.3110.281970.2363517X-RAY DIFFRACTION66.6188
2.311-2.4240.2462230.2164005X-RAY DIFFRACTION79.7435
2.424-2.5550.2541920.2064336X-RAY DIFFRACTION88.5586
2.555-2.710.2432270.2234110X-RAY DIFFRACTION89.9979
2.71-2.8970.2532450.2124277X-RAY DIFFRACTION100
2.897-3.1280.2562230.2043978X-RAY DIFFRACTION100
3.128-3.4260.2351940.1883695X-RAY DIFFRACTION99.9743
3.426-3.830.2111590.1682821X-RAY DIFFRACTION84.4671
3.83-4.4210.2091550.1652733X-RAY DIFFRACTION92.6532
4.421-5.410.2221230.1742511X-RAY DIFFRACTION100
5.41-7.6310.26850.2231981X-RAY DIFFRACTION99.9516
7.631-76.4520.233540.2321112X-RAY DIFFRACTION99.8288
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.541-0.2615-0.20390.61880.2340.62530.01090.0149-0.0159-0.0178-0.0171-0.01010.01280.02830.00620.00590.00140.00890.0060.0030.023447.1679-42.956552.7483
20.683-0.1726-0.16490.55050.21020.47860.0116-0.05820.00580.0326-0.0144-0.0235-0.02060.01250.00280.0173-0.00380.01020.00680.00090.014113.2504-45.812418.2738
Refinement TLS groupSelection: ALL

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