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- PDB-2wb3: The partial structure of a group A streptococcal phage-encoded ta... -

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Basic information

Entry
Database: PDB / ID: 2wb3
TitleThe partial structure of a group A streptococcal phage-encoded tail fibre hyaluronate lyase Hylp3
ComponentsHYALURONIDASE-PHAGE ASSOCIATED
KeywordsLYASE / HYALURONAN LYASE / PHAGE TAIL FIBRE / TRIPLE-STRANDED BETA- HELIX / HYALURONIDASE / SCARLET FEVER
Function / homologyHyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / Hyaluronidase-phage associated
Function and homology information
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMartinez-Fleites, C. / Black, G.W. / Turkenburg, J.P. / Smith, N.L. / Taylor, E.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structures of Two Truncated Phage-Tail Hyaluronate Lyases from Streptococcus Pyogenes Serotype M1.
Authors: Martinez-Fleites, C. / Smith, N.L. / Turkenburg, J.P. / Black, G.W. / Taylor, E.J.
History
DepositionFeb 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYALURONIDASE-PHAGE ASSOCIATED


Theoretical massNumber of molelcules
Total (without water)16,8541
Polymers16,8541
Non-polymers00
Water1,820101
1
A: HYALURONIDASE-PHAGE ASSOCIATED
x 6


Theoretical massNumber of molelcules
Total (without water)101,1256
Polymers101,1256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area66010 Å2
ΔGint-440.1 kcal/mol
Surface area42260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)49.476, 49.476, 241.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2077-

HOH

21A-2078-

HOH

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Components

#1: Protein HYALURONIDASE-PHAGE ASSOCIATED / HYLP3


Mass: 16854.125 Da / Num. of mol.: 1 / Fragment: HYALURONATE LYASE FRAGMENT, RESIDUES 214-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS SF370 / Plasmid: PET28A (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99Z19, hyaluronate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE IS A FRAGMENT, THE N-TERMINAL PORTION IS MISSING, THE STRUCTURE BEGINS AT RESIDUE 234.

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.5, 30 % (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 13481 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 36.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / % possible all: 51

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.385 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 679 5 %RANDOM
Rwork0.19 ---
obs0.192 12783 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 0 101 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221196
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9611619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00426.08746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19415217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.634154
X-RAY DIFFRACTIONr_chiral_restr0.1280.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021883
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0451.5783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87121261
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3873413
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7554.5358
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 27 -
Rwork0.296 480 -
obs--49.13 %

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