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- PDB-2yw0: Crystal structure of hyluranidase trimer at 2.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 2yw0
TitleCrystal structure of hyluranidase trimer at 2.6 A resolution
ComponentsHyaluronidase, phage associated
KeywordsLYASE / HYALURONAN LYASE / HYALURONIDASE
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 serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPrem Kumar, R. / Mishra, P. / Singh, N. / Perbandt, M. / Kaur, P. / Sharma, S. / Betzel, C. / Bhakuni, V. / Singh, T.P.
CitationJournal: Febs J. / Year: 2009
Title: Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose
Authors: Mishra, P. / Prem Kumar, R. / Ethayathulla, A.S. / Singh, N. / Sharma, S. / Perbandt, M. / Betzel, C. / Kaur, P. / Srinivasan, A. / Bhakuni, V. / Singh, T.P.
History
DepositionApr 18, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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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)36,4691
Polymers36,4691
Non-polymers00
Water1,946108
1
A: Hyaluronidase, phage associated

A: Hyaluronidase, phage associated

A: Hyaluronidase, phage associated


Theoretical massNumber of molelcules
Total (without water)109,4073
Polymers109,4073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area57900 Å2
ΔGint-232 kcal/mol
Surface area40260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.801, 58.801, 586.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hyaluronidase, phage associated


Mass: 36468.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Species: Streptococcus pyogenes / Strain: serotype M1 / Gene: hyl P2 / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A0M7, hyaluronate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: TRIS HCL, SODIUM FORMATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2006 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 12713 / Num. obs: 12713 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.038 / Net I/σ(I): 6.3
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C3F

2c3f


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.43 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.684 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21913 623 4.9 %RANDOM
Rwork0.1907 ---
all0.19442 12713 --
obs0.19304 12090 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.041 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å21.57 Å20 Å2
2--3.14 Å20 Å2
3----4.71 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 0 108 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222587
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9693486
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9525.421107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2715476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0851511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021909
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2650.2851
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21739
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.2407
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.281
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3691.51705
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.68222654
X-RAY DIFFRACTIONr_scbond_it5.5293986
X-RAY DIFFRACTIONr_scangle_it8.0514.5832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 53 -
Rwork0.215 870 -
obs--99.78 %

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