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- PDB-5bwi: Crystallographic structure of a bacterial heparanase -

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Basic information

Entry
Database: PDB / ID: 5bwi
TitleCrystallographic structure of a bacterial heparanase
ComponentsGlycoside Hydrolase Family 79
KeywordsHYDROLASE / glucuronidase
Function / homology
Function and homology information


Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Glycoside hydrolase family 44 domain-containing protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYu, X. / Blanchard, H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Functional and structural characterization of a heparanase.
Authors: Bohlmann, L. / Tredwell, G.D. / Yu, X. / Chang, C.W. / Haselhorst, T. / Winger, M. / Dyason, J.C. / Thomson, R.J. / Tiralongo, J. / Beacham, I.R. / Blanchard, H. / von Itzstein, M.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Structure summary
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside Hydrolase Family 79
B: Glycoside Hydrolase Family 79
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0896
Polymers90,8232
Non-polymers2664
Water21,8521213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-16 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.030, 125.030, 125.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Glycoside Hydrolase Family 79


Mass: 45411.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: DP46_278, DP55_3260 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A095J205, UniProt: Q63T97*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8 M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→31.29 Å / Num. obs: 129599 / % possible obs: 99.4 % / Redundancy: 14.54 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNZ

3vnz


Resolution: 1.6→31.29 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.519 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19187 6514 5 %RANDOM
Rwork0.16426 ---
obs0.16563 122996 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.6→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6319 0 17 1223 7559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196664
X-RAY DIFFRACTIONr_bond_other_d0.0010.026198
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9449159
X-RAY DIFFRACTIONr_angle_other_deg0.783314219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1823.75264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11815894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9151539
X-RAY DIFFRACTIONr_chiral_restr0.0840.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021581
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2261.783593
X-RAY DIFFRACTIONr_mcbond_other1.2211.7783591
X-RAY DIFFRACTIONr_mcangle_it2.022.6644506
X-RAY DIFFRACTIONr_mcangle_other2.022.6644507
X-RAY DIFFRACTIONr_scbond_it1.4691.8923071
X-RAY DIFFRACTIONr_scbond_other1.4681.8923072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.372.7884622
X-RAY DIFFRACTIONr_long_range_B_refined5.99616.7068745
X-RAY DIFFRACTIONr_long_range_B_other5.99616.7078746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 434 -
Rwork0.25 8438 -
obs--93.2 %

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