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- PDB-2dp5: Structure of streptococcus pyogenes bacteriophage-associated hyal... -

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Basic information

Entry
Database: PDB / ID: 2dp5
TitleStructure of streptococcus pyogenes bacteriophage-associated hyaluronate lyase Hylp2
ComponentsHyaluronidase
KeywordsLYASE / HYALURONAN LYASE / PHAGE TAIL FIBRE / TRIPLE-STRANDED BETA-HELIX / 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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsMishra, P. / Bhakuni, V. / Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Structure of streptococcus pyogenes bacteriophage-associated hyaluronate lyase Hylp2
Authors: Mishra, P. / Bhakuni, V. / Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
History
DepositionMay 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyaluronidase


Theoretical massNumber of molelcules
Total (without water)35,8341
Polymers35,8341
Non-polymers00
Water28816
1
A: Hyaluronidase

A: Hyaluronidase

A: Hyaluronidase


Theoretical massNumber of molelcules
Total (without water)107,5033
Polymers107,5033
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 area57710 Å2
ΔGint-253 kcal/mol
Surface area40030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.587, 59.587, 588.546
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


Mass: 35834.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: PET 21d / Gene (production host): hyl P2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A0M7, hyaluronate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5414 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 6, 2006 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 3.55→20 Å / Num. all: 5360 / Num. obs: 5360 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.128 / Net I/σ(I): 4.7
Reflection shellResolution: 3.55→3.65 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.285 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C3F

2c3f


Resolution: 3.55→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.885 / SU B: 45.134 / SU ML: 0.718 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23625 514 9.8 %RANDOM
Rwork0.22107 ---
obs0.22273 4747 98.95 %-
all-5360 --
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: 48.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 3.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 16 2534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212553
X-RAY DIFFRACTIONr_bond_other_d0.0020.022296
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9633440
X-RAY DIFFRACTIONr_angle_other_deg0.92135382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1013331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64415481
X-RAY DIFFRACTIONr_chiral_restr0.1020.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022863
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02480
X-RAY DIFFRACTIONr_nbd_refined0.2540.3445
X-RAY DIFFRACTIONr_nbd_other0.2420.31977
X-RAY DIFFRACTIONr_nbtor_other0.2970.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.5129
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.3140
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.3440
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.539
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0650.54
X-RAY DIFFRACTIONr_mcbond_it1.181.51639
X-RAY DIFFRACTIONr_mcangle_it2.2922614
X-RAY DIFFRACTIONr_scbond_it2.3073914
X-RAY DIFFRACTIONr_scangle_it4.3534.5826
LS refinement shellResolution: 3.55→3.639 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 38
Rwork0.249 324

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