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- PDB-2wh7: The partial structure of a group A streptpcoccal phage-encoded ta... -

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Basic information

Entry
Database: PDB / ID: 2wh7
TitleThe partial structure of a group A streptpcoccal phage-encoded tail fibre hyaluronate lyase Hylp2
ComponentsHYALURONIDASE-PHAGE ASSOCIATED
KeywordsHYDROLASE / TRIPLE-STRANDED BETA-HELIX / HYALURONAN LYASE / PHAGE TAIL FIBRE / GLYCOSIDASE / HYALURONIDASE / SCARLET FEVER
Function / homologyHyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / hyaluronoglucosaminidase / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / Hyaluronidase-phage associated
Function and homology information
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionMay 1, 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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)19,1191
Polymers19,1191
Non-polymers00
Water3,603200
1
A: HYALURONIDASE-PHAGE ASSOCIATED

A: HYALURONIDASE-PHAGE ASSOCIATED

A: HYALURONIDASE-PHAGE ASSOCIATED


Theoretical massNumber of molelcules
Total (without water)57,3563
Polymers57,3563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area28510 Å2
ΔGint-116.97 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.838, 50.838, 219.031
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-2048-

HOH

21A-2110-

HOH

31A-2111-

HOH

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Components

#1: Protein HYALURONIDASE-PHAGE ASSOCIATED / HYLP2


Mass: 19118.580 Da / Num. of mol.: 1 / Fragment: HYALURONATE LYASES FRAGMENT, RESIDUES 215-372
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: Q99ZZ7, hyaluronoglucosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE IS A FRAGMENT, THE N-TERMINAL PORTION IS MISSING, THE STRUCTURE BEGINS AS RESIDUE 235

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 2 M NACL, 10 % (W/V) PEG 6000;

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 23240 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 13 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C3F

2c3f


Resolution: 1.6→109.76 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.945 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1118 5.1 %RANDOM
Rwork0.212 ---
obs0.214 20606 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→109.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 0 200 1340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9721604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09326.2548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47215221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.449154
X-RAY DIFFRACTIONr_chiral_restr0.1240.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021881
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_it1.0721.5773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71221239
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0233415
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0954.5365
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: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 79 -
Rwork0.246 1448 -
obs--91.06 %

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