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- PDB-3ina: Crystal structure of heparin lyase I H151A mutant complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3ina
TitleCrystal structure of heparin lyase I H151A mutant complexed with a dodecasaccharide 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
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Non-polymer description / 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
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)45,2153
Polymers42,7671
Non-polymers2,4482
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.185, 63.433, 65.290
Angle α, β, γ (deg.)90.000, 112.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

#1: Protein Heparin lyase I /


Mass: 42767.297 Da / Num. of mol.: 1 / Mutation: H151A
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 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 2407.960 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,8,7/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-1-2-1-3-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}}}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 / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSGN, IDS AND NGN FORMS DODECASACCHARIDE HEPARIN. IT COMES FROM PORCINE INTESTINAL MUCOSA.
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. ALA 151 WAS ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. ALA 151 WAS ENGINEERED TO HIS. 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: 2.51 Å3/Da / Density % sol: 51.02 % / Mosaicity: 0.524 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% glycerol, 8% PEG 1500, Sarcosine, vapor diffusion, hanging drop, temperature 293K, pH 5.5, VAPOR DIFFUSION, HANGING DROP

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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: Apr 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33588 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Χ2: 1.91 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.976.70.23432861.351198.4
1.97-2.057.20.18833361.455199.9
2.05-2.147.40.15433391.4811100
2.14-2.257.50.1333581.5791100
2.25-2.397.50.10733661.7271100
2.39-2.587.50.09133631.831100
2.58-2.847.50.07833472.071100
2.84-3.257.50.06433962.4321100
3.25-4.097.40.05233812.582199.9
4.09-507.10.04734162.526198.9

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Processing

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

3imn


Resolution: 1.9→36.82 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3255 9.7 %RANDOM
Rwork0.194 ---
all-33326 --
obs-32566 97.1 %-
Displacement parametersBiso max: 91.84 Å2 / Biso mean: 30.996 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1--10.521 Å20 Å2-7.897 Å2
2--7.813 Å20 Å2
3---2.708 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 146 231 3328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.547
X-RAY DIFFRACTIONc_mcbond_it1.2871.5
X-RAY DIFFRACTIONc_scbond_it2.1272
X-RAY DIFFRACTIONc_mcangle_it1.9912
X-RAY DIFFRACTIONc_scangle_it3.2512.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4heparin.paramheparin.top
X-RAY DIFFRACTION5CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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