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- PDB-5jmf: Heparinase III-BT4657 gene product -

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Basic information

Entry
Database: PDB / ID: 5jmf
TitleHeparinase III-BT4657 gene product
ComponentsHeparinase III protein
KeywordsLYASE / HeparinaseIII / BT4657 gene product / Bacteroides thetaiotaomicron
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
Heparin-sulfate lyase, N-terminal / Heparinase II/III N-terminus / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel ...Heparin-sulfate lyase, N-terminal / Heparinase II/III N-terminus / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Heparinase III protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsUlaganathan, T.S. / Shi, R. / Yao, D. / Garron, M.-L. / Cherney, M. / Cygler, M.
CitationJournal: Glycobiology / Year: 2017
Title: Conformational flexibility of PL12 family heparinases: structure and substrate specificity of heparinase III from Bacteroides thetaiotaomicron (BT4657).
Authors: Ulaganathan, T. / Shi, R. / Yao, D. / Gu, R.X. / Garron, M.L. / Cherney, M. / Tieleman, D.P. / Sterner, E. / Li, G. / Li, L. / Linhardt, R.J. / Cygler, M.
History
DepositionApr 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparinase III protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3314
Polymers77,0921
Non-polymers2393
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint1 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.690, 45.741, 80.514
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1202-

HOH

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Components

#1: Protein Heparinase III protein


Mass: 77092.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89YS4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 100mM Bis-Tris pH 5.5, 200mM Magnesium chloride,500mM NDSB-201 as additive inn crystallization drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.85→20.503 Å / Num. obs: 58055 / % possible obs: 98.7 % / Redundancy: 3.6 % / Net I/σ(I): 27.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.854→20.503 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.32
RfactorNum. reflection% reflection
Rfree0.2032 2903 5.07 %
Rwork0.1646 --
obs0.1665 57221 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.854→20.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 15 536 5764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015441
X-RAY DIFFRACTIONf_angle_d0.9837378
X-RAY DIFFRACTIONf_dihedral_angle_d13.0673175
X-RAY DIFFRACTIONf_chiral_restr0.06744
X-RAY DIFFRACTIONf_plane_restr0.007953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8541-1.88450.2521200.2512286X-RAY DIFFRACTION89
1.8845-1.9170.26461230.23192570X-RAY DIFFRACTION98
1.917-1.95180.26421270.21912523X-RAY DIFFRACTION98
1.9518-1.98930.25431460.21282590X-RAY DIFFRACTION99
1.9893-2.02990.2741290.19872522X-RAY DIFFRACTION98
2.0299-2.0740.26041240.1922601X-RAY DIFFRACTION99
2.074-2.12220.22991340.18512568X-RAY DIFFRACTION99
2.1222-2.17520.23681500.17262592X-RAY DIFFRACTION99
2.1752-2.23390.22411340.16552564X-RAY DIFFRACTION99
2.2339-2.29960.19461460.17082587X-RAY DIFFRACTION99
2.2996-2.37370.22031580.16112600X-RAY DIFFRACTION100
2.3737-2.45840.2611190.18972597X-RAY DIFFRACTION100
2.4584-2.55660.25391480.18142609X-RAY DIFFRACTION100
2.5566-2.67280.23871360.18232632X-RAY DIFFRACTION100
2.6728-2.81340.21471550.17172600X-RAY DIFFRACTION100
2.8134-2.98910.19981300.17492634X-RAY DIFFRACTION100
2.9891-3.21910.20011590.16392626X-RAY DIFFRACTION100
3.2191-3.54160.18691490.15142618X-RAY DIFFRACTION100
3.5416-4.05060.16971590.14252627X-RAY DIFFRACTION100
4.0506-5.09040.15531080.12992714X-RAY DIFFRACTION100
5.0904-20.50410.1911490.16452658X-RAY DIFFRACTION97
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)
12.76050.19420.36552.23010.55112.04680.2049-0.7632-0.67070.57390.0622-0.12330.5888-0.0621-0.14940.43910.0125-0.01880.37990.16850.402928.215118.891464.4618
24.1107-1.8531-0.67110.3389-0.1535-0.2944-0.0773-0.03840.05670.06470.03470.0277-0.0549-0.03470.03180.21590.0128-0.00180.2397-0.04650.24452.753624.991651.7444
32.8941-0.34940.79131.85990.04472.0017-0.0803-0.28780.11080.2448-0.0205-0.1843-0.06840.01460.06640.1579-0.0017-0.00270.1929-0.00990.178482.8921.405961.1693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 395 )
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 666 )

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