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- PDB-3in9: Crystal structure of heparin lyase I complexed with disaccharide ... -

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Basic information

Entry
Database: PDB / ID: 3in9
TitleCrystal structure of heparin lyase I complexed with disaccharide heparin
ComponentsHeparin lyase I
KeywordsLYASE / jelly roll
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
duf1285 like fold - #20 / Polysaccharide lyase / Polysaccharide lyase / duf1285 like fold / Jelly Rolls - #200 / Jelly Rolls / Roll / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HEPARIN DISACCHARIDE I-S, / Heparin lyase I
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHan, Y.H. / Ryu, K.S. / Kim, H.Y. / 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 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparin lyase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0294
Polymers42,8341
Non-polymers1,1953
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heparin lyase I
hetero molecules

A: Heparin lyase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0598
Polymers85,6692
Non-polymers2,3906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5570 Å2
ΔGint-105 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.789, 63.531, 65.204
Angle α, β, γ (deg.)90.000, 115.470, 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: WAL2926 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89YQ6*PLUS
#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.: 2
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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDISACCHARIDE HEPARIN, H1S, COMES FROM PORCINE INTESTINAL MUCOSA
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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 % / Mosaicity: 0.28 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% glycerol, 20% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 28413 / Num. obs: 28121 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Χ2: 1.798 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.073.40.10227061.23395.7
2.07-2.153.50.09227881.31899.1
2.15-2.253.60.08427701.47198.6
2.25-2.373.70.07928191.65399.3
2.37-2.523.70.07428361.77699.5
2.52-2.713.80.07128051.49699.6
2.71-2.993.90.0728181.77699.5
2.99-3.4240.06628392.14899.8
3.42-4.3140.06228642.34999.8
4.31-503.90.06128762.45198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.09 Å31.76 Å
Translation2.09 Å31.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IMN

3imn


Resolution: 2→31.77 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.827 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2789 9.9 %RANDOM
Rwork0.183 ---
obs-28059 99.3 %-
Displacement parametersBiso max: 80.12 Å2 / Biso mean: 27.791 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1--7.449 Å20 Å2-6.533 Å2
2--6.523 Å20 Å2
3---0.926 Å2
Refinement stepCycle: LAST / Resolution: 2→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 71 303 3352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.504
X-RAY DIFFRACTIONc_mcbond_it1.3331.5
X-RAY DIFFRACTIONc_scbond_it1.9712
X-RAY DIFFRACTIONc_mcangle_it2.0282
X-RAY DIFFRACTIONc_scangle_it2.9662.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION4heparin.paramheparin.top
X-RAY DIFFRACTION5CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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