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

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Basic information

Entry
Database: PDB / ID: 9grw
TitleStructure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor
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: 1.85 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 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,41341
Polymers87,1492
Non-polymers3,26439
Water12,088671
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes at expected position for a monomer by SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-385 kcal/mol
Surface area32870 Å2
Unit cell
Length a, b, c (Å)140.194, 91.485, 73.448
Angle α, β, γ (deg.)90, 95.46, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

21B-670-

HOH

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

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: A / Label asym-ID: A / Auth seq-ID: 8 - 373 / Label seq-ID: 8 - 373

Dom-ID
1
2

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

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Components

#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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.28 %
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: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953738 Å / Relative weight: 1
ReflectionResolution: 1.85→54.29 Å / Num. obs: 78798 / % possible obs: 99.92 % / Redundancy: 7 % / CC1/2: 0.966 / Rmerge(I) obs: 0.387 / Rpim(I) all: 0.159 / Net I/σ(I): 6.4
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 2.965 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3893 / CC1/2: 0.351 / Rpim(I) all: 1.207

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→54.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.149 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2468 3925 4.981 %
Rwork0.2103 74868 -
all0.212 --
obs-78793 99.914 %
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: 24.432 Å2
Baniso -1Baniso -2Baniso -3
1--0.193 Å2-0 Å2-0.215 Å2
2--0.134 Å20 Å2
3---0.098 Å2
Refinement stepCycle: LAST / Resolution: 1.85→54.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5911 0 177 671 6759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126223
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165695
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.848400
X-RAY DIFFRACTIONr_angle_other_deg0.4461.79713175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3985737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.973532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.359101065
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.94910282
X-RAY DIFFRACTIONr_chiral_restr0.0610.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021413
X-RAY DIFFRACTIONr_nbd_refined0.20.21059
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25231
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22935
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2540
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.227
X-RAY DIFFRACTIONr_nbd_other0.1630.2140
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.226
X-RAY DIFFRACTIONr_mcbond_it1.21.6232969
X-RAY DIFFRACTIONr_mcbond_other1.1811.6152955
X-RAY DIFFRACTIONr_mcangle_it1.9942.8953687
X-RAY DIFFRACTIONr_mcangle_other1.9942.8953688
X-RAY DIFFRACTIONr_scbond_it1.5881.9133254
X-RAY DIFFRACTIONr_scbond_other1.3781.7953125
X-RAY DIFFRACTIONr_scangle_it2.5073.4144713
X-RAY DIFFRACTIONr_scangle_other2.343.2044522
X-RAY DIFFRACTIONr_lrange_it5.37217.7916987
X-RAY DIFFRACTIONr_lrange_other5.1317.0516820
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0512084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088110.0501
12AX-RAY DIFFRACTIONLocal ncs0.088110.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8970.3442930.3315498X-RAY DIFFRACTION98.9576
1.897-1.9490.3612850.3465388X-RAY DIFFRACTION99.9824
1.949-2.0060.2892760.2725159X-RAY DIFFRACTION100
2.006-2.0670.3172550.2815104X-RAY DIFFRACTION99.9627
2.067-2.1350.2992580.2654935X-RAY DIFFRACTION100
2.135-2.210.2582720.2224723X-RAY DIFFRACTION100
2.21-2.2930.3012550.294606X-RAY DIFFRACTION100
2.293-2.3870.2282180.24433X-RAY DIFFRACTION100
2.387-2.4920.2462010.2024256X-RAY DIFFRACTION100
2.492-2.6140.262050.2034120X-RAY DIFFRACTION100
2.614-2.7550.2532050.2023825X-RAY DIFFRACTION100
2.755-2.9210.2421980.1983652X-RAY DIFFRACTION100
2.921-3.1230.2241750.1983444X-RAY DIFFRACTION100
3.123-3.3720.2181580.1923234X-RAY DIFFRACTION100
3.372-3.6920.2071600.172960X-RAY DIFFRACTION100
3.692-4.1260.2061530.152665X-RAY DIFFRACTION100
4.126-4.7590.171150.1312362X-RAY DIFFRACTION100
4.759-5.8180.213990.1652033X-RAY DIFFRACTION100
5.818-8.1810.241870.2061582X-RAY DIFFRACTION100
8.181-54.290.265570.232889X-RAY DIFFRACTION99.8944
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)
10.82450.3049-0.12230.8532-0.24890.64930.03240.06740.0196-0.0287-0.01680.0312-0.01980.0037-0.01560.0370.00790.01460.00860.00130.0083-20.2077-0.072254.6677
20.6676-0.2775-0.2040.80980.2540.73820.00730.0345-0.0261-0.0158-0.03630.00510.00370.00140.0290.0248-0.00830.01510.02260.00280.0162-22.5164-42.920852.7861
Refinement TLS groupSelection: ALL

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