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- PDB-3imn: Crystal structure of heparin lyase I from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 3imn
TitleCrystal structure of heparin lyase I from Bacteroides thetaiotaomicron
ComponentsHeparin lyase I
KeywordsLYASE / jelly roll
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
duf1285 like fold - #20 / duf1285 like fold / Polysaccharide lyase / Polysaccharide lyase / Jelly Rolls - #200 / Jelly Rolls / Roll / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsHan, Y.H. / Ryu, K.S. / Jeon, Y.H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural snapshots of heparin depolymerization by heparin lyase I
Authors: Han, Y.H. / Garron, M.L. / Kim, H.Y. / Kim, W.S. / Zhang, Z. / Ryu, K.S. / Shaya, D. / Xiao, Z. / Cheong, C. / Kim, Y.S. / Linhardt, R.J. / Jeon, Y.H. / Cygler, M.
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heparin lyase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4518
Polymers42,8341
Non-polymers6167
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.921, 68.712, 61.306
Angle α, β, γ (deg.)90.000, 105.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heparin lyase I


Mass: 42834.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: WAL 2926 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89YQ6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THE TWO ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THE TWO RESIDUES AT THE C-TERMINAL OF THE SEQUENCE, LEU 377 AND GLU 378, ARE EXPRESSION TAGS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 % / Mosaicity: 0.583 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Na citrate pH 5.5, 2.0M Ammonium sulfate, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPAL/PLS 6B20.97905, 0.97924, 0.97136
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 18, 2006
Bruker AXIOM 2002CCDMar 28, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979051
30.979241
40.971361
ReflectionRedundancy: 6.4 % / Av σ(I) over netI: 37.14 / Number: 87493 / Rmerge(I) obs: 0.075 / Χ2: 1.04 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 13715 / % possible obs: 88.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.110.0421.7966.5
4.275.3899.710.0461.2377
3.734.2799.410.0581.1347
3.393.7399.310.080.9527.1
3.153.3998.810.1160.9677
2.963.1595.110.1530.7556.5
2.822.9685.510.1890.7296.1
2.692.8276.810.2420.7355.5
2.592.696810.2550.8075.1
2.52.5960.210.2780.824.6
ReflectionResolution: 1.8→58.93 Å / Num. all: 43830 / Num. obs: 40417 / % possible obs: 92.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Χ2: 2.33 / Net I/av σ(I): 37.143 / Net I/σ(I): 21.3 / Num. measured all: 177991
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.863.20.17824151.10255.3
1.86-1.943.70.16237541.38486.9
1.94-2.0340.13340661.65993.2
2.03-2.134.20.1142271.87496.2
2.13-2.274.40.09642282.02596.8
2.27-2.444.50.08442482.26297.4
2.44-2.694.60.07243022.4598.3
2.69-3.084.80.06143652.76299
3.08-3.884.90.04943693.14699.7
3.88-5050.04344433.07899.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.81→36.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.884 / SU B: 2.38 / SU ML: 0.074 / SU R Cruickshank DPI: 0.121 / SU Rfree: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2052 5.1 %RANDOM
Rwork0.179 38365 --
obs0.181 40417 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.48 Å2 / Biso mean: 27.651 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20.51 Å2
2---1.33 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.81→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 31 259 3263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223072
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.964157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43724.414145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72215527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7711515
X-RAY DIFFRACTIONr_chiral_restr0.1910.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212343
X-RAY DIFFRACTIONr_mcbond_it1.4021.51848
X-RAY DIFFRACTIONr_mcangle_it2.29722985
X-RAY DIFFRACTIONr_scbond_it3.33631224
X-RAY DIFFRACTIONr_scangle_it5.214.51172
LS refinement shellResolution: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 125 -
Rwork0.221 2099 -
all-2224 -
obs--70.36 %

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