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- PDB-2fuq: Crystal Structure of Heparinase II -

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Basic information

Entry
Database: PDB / ID: 2fuq
TitleCrystal Structure of Heparinase II
Componentsheparinase II protein
KeywordsSUGAR BINDING PROTEIN / alpha plus beta
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
FORMIC ACID / PHOSPHATE ION / : / Heparin and heparin-sulfate lyase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsShaya, D. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of Heparinase II from Pedobacter heparinus and Its Complex with a Disaccharide Product.
Authors: Shaya, D. / Tocilj, A. / Li, Y. / Myette, J. / Venkataraman, G. / Sasisekharan, R. / Cygler, M.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 23, 2016Group: Derived calculations / Non-polymer description
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 / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,14511
Polymers169,4172
Non-polymers1,7289
Water16,718928
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.046, 119.339, 200.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe bilogical assembly is a homodimer present in the asymetric unit

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein heparinase II protein


Mass: 84708.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (bacteria) / Gene: hep b / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 924923, UniProt: C6XZB6*PLUS
#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.: 2
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

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Non-polymers , 4 types, 935 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 17% PEG 3350, 0.2M sodium phosphate , pH 5.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 112668 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.051 / Net I/σ(I): 30.54
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 10.1 / Rsym value: 0.145 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→102.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.594 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23456 4640 5.1 %RANDOM
Rwork0.19478 ---
obs0.19679 86490 98.73 %-
all-86490 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.634 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--5.56 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.15→102.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11956 0 103 928 12987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.96516757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9351492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8523.916572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.532152086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7091568
X-RAY DIFFRACTIONr_chiral_restr0.0750.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029450
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.26031
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.28342
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.21095
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3371.57665
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.577211972
X-RAY DIFFRACTIONr_scbond_it0.9535491
X-RAY DIFFRACTIONr_scangle_it1.4264.54785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 354 -
Rwork0.208 6290 -
obs--98.21 %
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)
11.2656-0.1601-0.79841.10870.26083.1471-0.0766-0.1917-0.01410.37340.06460.1701-0.2683-0.58870.012-0.02110.08390.0395-0.02230.0344-0.074226.05244.028989.5898
20.99570.03750.04870.81170.02412.6197-0.0226-0.07670.00320.06090.012-0.0941-0.10280.51550.0105-0.1757-0.0250.0035-0.13640.014-0.117355.299440.196369.67
30.8166-0.22010.33480.76390.10993.26520.0094-0.0047-0.1187-0.0097-0.0398-0.07640.42840.48290.0304-0.10170.05220.0129-0.17110.0082-0.068553.061728.300745.4032
41.36240.4416-0.91451.1857-0.53352.4947-0.09510.2369-0.0484-0.34820.0082-0.1132-0.0772-0.07960.0869-0.04710.010.0197-0.221-0.0243-0.097446.63943.578910.7639
51.3648-0.0058-0.00120.75130.15112.3477-0.01090.07750.0237-0.0904-0.06720.1063-0.1154-0.8250.0781-0.16760.0459-0.00470.0923-0.0725-0.110917.441840.30830.8242
61.29210.42530.63150.96860.05983.34670.0164-0.1101-0.18060.0206-0.08880.11520.3872-0.86660.0724-0.1155-0.1140.02190.0815-0.0282-0.052519.575128.468555.0968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 3601 - 335
2X-RAY DIFFRACTION2AA361 - 675336 - 650
3X-RAY DIFFRACTION3AA676 - 772651 - 747
4X-RAY DIFFRACTION4BB26 - 3601 - 335
5X-RAY DIFFRACTION5BB361 - 675336 - 650
6X-RAY DIFFRACTION6BB676 - 772651 - 747

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