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- PDB-6lja: Crystal Structure of exoHep from Bacteroides intestinalis DSM 173... -

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Basic information

Entry
Database: PDB / ID: 6lja
TitleCrystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product
ComponentsHeparinase II/III-like protein
KeywordsLYASE / heparin / heparan sulfate / heparinase
Function / homologyHeparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / lyase activity / Immunoglobulin-like fold / HEPARIN DISACCHARIDE I-S, / Heparinase II/III-like protein
Function and homology information
Biological speciesBacteroides intestinalis DSM 17393 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.978 Å
AuthorsZhang, Q.D. / Cao, H.Y. / Wei, L. / Li, F.C. / Zhang, Y.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570071 China
National Natural Science Foundation of China (NSFC)31971201 China
CitationJournal: Nat Commun / Year: 2021
Title: Discovery of exolytic heparinases and their catalytic mechanism and potential application.
Authors: Zhang, Q. / Cao, H.Y. / Wei, L. / Lu, D. / Du, M. / Yuan, M. / Shi, D. / Chen, X. / Wang, P. / Chen, X.L. / Chi, L. / Zhang, Y.Z. / Li, F.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heparinase II/III-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7154
Polymers100,0571
Non-polymers6583
Water16,087893
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-18 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.475, 108.333, 128.685
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 Heparinase II/III-like protein


Mass: 100057.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria)
Gene: BACINT_00178 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3C5J6
#2: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose / HEPARIN DISACCHARIDE I-S /


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 577.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with ring modification on monosaccharide components
References: HEPARIN DISACCHARIDE I-S,
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% (w/v) PEG 1500, 0.1 M MMT (DL-malic acid, MES, and Tris), pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.978→34.77 Å / Num. obs: 58145 / % possible obs: 98.84 % / Redundancy: 6.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Net I/σ(I): 15.17
Reflection shellResolution: 1.978→2.049 Å / Rmerge(I) obs: 0.309 / Num. unique obs: 5338 / CC1/2: 0.981 / Rpim(I) all: 0.133 / Rrim(I) all: 0.11

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.978→34.768 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.17
RfactorNum. reflection% reflection
Rfree0.1851 2829 4.87 %
Rwork0.1463 --
obs0.1482 58118 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.24 Å2 / Biso mean: 22.65 Å2 / Biso min: 8.89 Å2
Refinement stepCycle: final / Resolution: 1.978→34.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 37 893 7720
Biso mean--26.6 28.96 -
Num. residues----841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077018
X-RAY DIFFRACTIONf_angle_d1.0529542
X-RAY DIFFRACTIONf_chiral_restr0.075999
X-RAY DIFFRACTIONf_plane_restr0.0051244
X-RAY DIFFRACTIONf_dihedral_angle_d13.0522558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9783-2.01250.21581000.1601230783
2.0125-2.0490.20971580.1482773100
2.049-2.08840.19911490.14432713100
2.0884-2.13110.17861350.14292801100
2.1311-2.17740.16411360.13762737100
2.1774-2.2280.18081380.14042760100
2.228-2.28380.19071280.1462773100
2.2838-2.34550.21281560.1473272999
2.3455-2.41450.22831430.1516275999
2.4145-2.49240.21271710.1505274399
2.4924-2.58150.21061530.14652798100
2.5815-2.68480.19571490.14992741100
2.6848-2.80690.19561280.1485277099
2.8069-2.95480.18221430.1531278899
2.9548-3.13980.19841360.15372801100
3.1398-3.38210.20981470.15242795100
3.3821-3.72210.16651290.14832855100
3.7221-4.25990.17181350.13422844100
4.2599-5.36380.14871670.1262849100
5.3638-34.7680.17011280.1631295398

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