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- PDB-2c3f: The structure of a group A streptococcal phage-encoded tail-fibre... -

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Basic information

Entry
Database: PDB / ID: 2c3f
TitleThe structure of a group A streptococcal phage-encoded tail-fibre showing hyaluronan lyase activity.
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 / MAD / Resolution: 1.81 Å
AuthorsTaylor, E.J. / Smith, N.L. / Linsay, A.-M. / Charnock, S.J. / Turkenburg, J.P. / Dodson, E.J. / Davies, G.J. / Black, G.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of a Group a Streptococcal Phage-Encoded Virulence Factor Reveals Catalytically Active Triple-Stranded Beta-Helix
Authors: Smith, N.L. / Taylor, E.J. / Linsay, A.-M. / Charnock, S.J. / Turkenburg, J.P. / Dodson, E.J. / Davies, G.J. / Black, G.W.
History
DepositionOct 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYALURONIDASE, PHAGE ASSOCIATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6353
Polymers38,5891
Non-polymers462
Water4,756264
1
A: HYALURONIDASE, PHAGE ASSOCIATED
hetero molecules

A: HYALURONIDASE, PHAGE ASSOCIATED
hetero molecules

A: HYALURONIDASE, PHAGE ASSOCIATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9069
Polymers115,7683
Non-polymers1386
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.534, 58.534, 586.585
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2049-

HOH

21A-2075-

HOH

31A-2092-

HOH

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Components

#1: Protein HYALURONIDASE, PHAGE ASSOCIATED / / HYLP1


Mass: 38589.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS SF370 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834-BL21 / References: UniProt: Q9A0M7, hyaluronate lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE ABOVE CONTAINS ADDITIONAL RESIDUES DERIVED FROM THE CLONING VECTOR ...THE SEQUENCE ABOVE CONTAINS ADDITIONAL RESIDUES DERIVED FROM THE CLONING VECTOR MGSSHHHHHHSSGLVPRGSHMS RESIDUES SENIPLRVQ CORRESPOND TO RESIDUES 2-10 GIVE IN THE GENBANK SEQUENCE. THE REST OF THE SEQUENCE IS AS THE GENBANK SEQUENCE. THE N-TERMINAL PORTION OF THE CONSTRUCT IS DISORDERED IN THE STRUCTURE AND SO THE FIRST RESIDUE IN THE PDB IS RESIDUE 7.

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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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growDetails: 3.25M SODIUM FORMATE, PROTEIN CONCENTRATION 10-20 MG/ML IN 20MM HEPES 50MM CALCIUM CHLORIDE. 1 MICROLITRE OF MOTHER LIQUOR MIXED WITH 1 MICROLITRE OF PROTEIN.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2003 / Details: FIXED RADII TOROIDAL MIRROR
RadiationMonochromator: GE(220) CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→195.52 Å / Num. obs: 34533 / % possible obs: 98.7 % / Observed criterion σ(I): 3.9 / Redundancy: 5.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→196.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.441 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1816 5 %RANDOM
Rwork0.188 ---
obs0.19 34533 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20.65 Å20 Å2
2--1.3 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 1.81→196.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 2 264 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222461
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9693316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71125.446101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10615448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5121511
X-RAY DIFFRACTIONr_chiral_restr0.1290.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021809
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2777
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21693
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.2429
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.2116
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0640.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.51587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8322539
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9423874
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9864.5777
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: 1.81→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 122 -
Rwork0.24 2276 -
obs--90.12 %

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