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- PDB-3e80: Structure of Heparinase II complexed with heparan sulfate degrada... -

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Basic information

Entry
Database: PDB / ID: 3.0E+80
TitleStructure of Heparinase II complexed with heparan sulfate degradation disaccharide product
ComponentsHeparinase II protein
KeywordsSUGAR BINDING PROTEIN / LYASE / alpha and beta lyase fold / alpha6/alpha6 incomplete toroid
Function / homology
Function and homology information


heparin lyase / heparin lyase activity / heparin-sulfate lyase / heparin-sulfate lyase activity / heparin catabolic process / heparin binding / periplasmic space / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2750 / Heparinase II, C-terminal / Heparinase II C-terminal domain / Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase ...Immunoglobulin-like - #2750 / Heparinase II, C-terminal / Heparinase II C-terminal domain / Heparinase II, N-terminal / Domain of unknown function (DUF4962) / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Heparin and heparin-sulfate lyase / Heparin and heparin-sulfate lyase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsShaya, D. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate.
Authors: Shaya, D. / Zhao, W. / Garron, M.L. / Xiao, Z. / Cui, Q. / Zhang, Z. / Sulea, T. / Linhardt, R.J. / Cygler, M.
History
DepositionAug 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 30, 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: Heparinase II protein
B: Heparinase II protein
C: Heparinase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,96921
Polymers254,8763
Non-polymers4,09318
Water9,656536
1
A: Heparinase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4188
Polymers84,9591
Non-polymers1,4597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heparinase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3237
Polymers84,9591
Non-polymers1,3646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heparinase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2286
Polymers84,9591
Non-polymers1,2695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)201.280, 209.360, 59.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-847-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Heparinase II protein


Mass: 84958.664 Da / Num. of mol.: 3 / Fragment: UNP residues 24-772 / Source method: isolated from a natural source / Source: (natural) Pedobacter heparinus (bacteria) / References: UniProt: Q46080, UniProt: C6XZB6*PLUS

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Sugars , 2 types, 6 molecules

#2: Polysaccharide alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha- ...alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 634.535 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-4DGlcpAa1-2[LRhapa1-4]DManpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a1122h-1a_1-5][a2122A-1a_1-5][a212h-1a_1-5][a2211m-1a_1-5]/1-2-3-4/a2-b1_a4-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpA]{[(4+1)][b-L-4-deoxy-Arap]{}}[(4+1)][a-L-Rhap]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 379.317 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a21eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][a-L-4-deoxy-IdopA]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 548 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#6: 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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Details

Sequence detailsTHE AUTHOR'S NATIVE CLONE WAS SEQUENCED AND REVEALED ALA RATHER THAN PRO AT THIS POSITION. THE ...THE AUTHOR'S NATIVE CLONE WAS SEQUENCED AND REVEALED ALA RATHER THAN PRO AT THIS POSITION. THE AUTHORS BELIEVE THAT PRO IS A MISTAKE IN THE UNP DATABASE

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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: 2.45 Å3/Da / Density % sol: 49.75 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→37.57 Å / Num. obs: 103320 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Redundancy: 4.62 % / Rmerge(I) obs: 0.134 / Χ2: 0.99 / Net I/σ(I): 8.3 / Scaling rejects: 3607
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.35-2.433.810.3024.43582293721.0590
2.43-2.534.670.2994.848064102651.0498.7
2.53-2.654.70.294.948543102841.0199
2.65-2.794.690.2645.148650103351.0199.2
2.79-2.964.680.2465.449084104431.0199.1
2.96-3.194.710.2056.348825103161.0299.2
3.19-3.514.690.1567.749288104411.0299.2
3.51-4.024.70.10111.249860104820.9799.2
4.02-5.064.740.06915.350763105310.9298.9
5.06-37.574.720.05915.951933108510.8798.1

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUQ

1fuq


Resolution: 2.35→37.57 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.801 / SU B: 21.972 / SU ML: 0.247 / SU R Cruickshank DPI: 0.511 / SU Rfree: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.492 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5152 5 %RANDOM
Rwork0.229 ---
obs0.231 103320 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 57.09 Å2 / Biso mean: 24.105 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.35→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17931 0 249 536 18716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218651
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.97125263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78752238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96723.916858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.661153099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.01115102
X-RAY DIFFRACTIONr_chiral_restr0.0930.22667
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114211
X-RAY DIFFRACTIONr_mcbond_it0.3141.511148
X-RAY DIFFRACTIONr_mcangle_it0.589217964
X-RAY DIFFRACTIONr_scbond_it1.1537503
X-RAY DIFFRACTIONr_scangle_it1.8014.57299
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 354 -
Rwork0.362 6464 -
all-6818 -
obs--88.44 %
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)
12.37591.0784-1.11831.2889-0.53461.06930.0878-0.16220.15510.0539-0.0985-0.1613-0.09880.24720.0107-0.1193-0.0098-0.03-0.0256-0.0063-0.05939.273115.47713.756
21.8087-0.1144-0.10761.04050.04250.9561-0.0069-0.0689-0.397-0.0096-0.0403-0.03490.15360.11450.0471-0.11920.0043-0.01-0.12630.0261-0.04719.65286.05317.02
33.4825-1.092-0.18931.7996-0.38561.513-0.0345-0.3862-0.67770.1669-0.00130.24670.1577-0.13860.0359-0.1015-0.0038-0.0156-0.04230.0784-0.0072-4.67987.96728.862
43.7399-0.364-0.79881.45020.03311.17560.14070.01310.71040.06390.00490.2801-0.1318-0.2644-0.1455-0.09810.02760.0168-0.03260.05030.198661.032149.62942.901
51.7472-0.1238-0.31221.2786-0.02660.72-0.02050.0695-0.2805-0.0258-0.01070.08110.0588-0.10340.0311-0.1317-0.0063-0.0226-0.09240.00410.032180.995120.76637.424
63.34290.9395-0.16921.61091.00891.2148-0.01190.405-0.4135-0.1525-0.085-0.01090.13340.15210.0969-0.06070.0141-0.0073-0.0415-0.0140.0593105.299123.77825.876
72.9985-1.27930.82151.7168-0.56931.35010.03450.0137-0.14440.02920.0248-0.08830.04520.1579-0.0594-0.1205-0.00180.029-0.0780.0048-0.0606139.696128.77441.945
82.2888-0.1866-0.14311.55960.15921.1522-0.0132-0.08020.60260.07480.0224-0.0984-0.10350.1012-0.0092-0.12560.00770.0366-0.12630.01410.1418119.885158.240.898
93.33880.9970.1631.8881-0.71751.20180.03320.38720.7187-0.1498-0.05170.3123-0.1728-0.140.0185-0.05720.0235-0.0065-0.05160.11580.231295.692157.18428.628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 3603 - 337
2X-RAY DIFFRACTION2AA361 - 675338 - 652
3X-RAY DIFFRACTION3AA676 - 772653 - 749
4X-RAY DIFFRACTION4BB26 - 3603 - 337
5X-RAY DIFFRACTION5BB361 - 675338 - 652
6X-RAY DIFFRACTION6BB676 - 772653 - 749
7X-RAY DIFFRACTION7CC26 - 3603 - 337
8X-RAY DIFFRACTION8CC361 - 675338 - 652
9X-RAY DIFFRACTION9CC676 - 772653 - 749

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