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- PDB-6wv2: Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: P... -

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Basic information

Entry
Database: PDB / ID: 6wv2
TitleCrystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism
ComponentsHyaluronan Lyase
KeywordsLYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / hyaluronoglucosaminidase / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / symbiont entry into host cell via disruption of host cell envelope / virion component
Similarity search - Function
Hyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain
Similarity search - Domain/homology
NICKEL (II) ION / Hyaluronoglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pyogenes phage H4489A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsDeivanayagam, C. / Schormann, N.
CitationJournal: To Be Published
Title: Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism
Authors: Lee, J.H. / Schormann, N. / Rajashankar, K.R. / Deivanaygam, C.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyaluronan Lyase
B: Hyaluronan Lyase
C: Hyaluronan Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6564
Polymers94,5973
Non-polymers591
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52260 Å2
ΔGint-246 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.451, 86.789, 168.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 107 through 377)
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 107 - 377 / Label seq-ID: 21 - 291

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 107 through 377)AA
2chain BBB
3chain CCC

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Components

#1: Protein Hyaluronan Lyase / HylP / Hyaluronate Lyase


Mass: 31532.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes phage H4489A (virus)
Gene: HYLP1, HYLP / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15316, hyaluronate lyase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 52.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% (V/V) 2-PROPANOL AND 20% (W/V) PEG 4000 IN 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50393 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.337 / Net I/av σ(I): 26.9 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 4986 / Χ2: 1.35 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C3F

2c3f


Resolution: 2.21→38.609 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 2383 4.77 %
Rwork0.2127 47657 -
obs-50040 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.15 Å2 / Biso mean: 42.9976 Å2 / Biso min: 16.18 Å2
Refinement stepCycle: final / Resolution: 2.21→38.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 1 282 6383
Biso mean--65.83 41.79 -
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066181
X-RAY DIFFRACTIONf_angle_d0.9978299
X-RAY DIFFRACTIONf_chiral_restr0.055942
X-RAY DIFFRACTIONf_plane_restr0.0051074
X-RAY DIFFRACTIONf_dihedral_angle_d7.5163817
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3806X-RAY DIFFRACTION13.761TORSIONAL
12B3806X-RAY DIFFRACTION13.761TORSIONAL
13C3806X-RAY DIFFRACTION13.761TORSIONAL
LS refinement shellResolution: 2.21→2.289 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3134 209 -
Rwork0.2987 4729 -
obs--99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0065-0.00140.1344-0.0826-0.05282.30350.060.24210.259-0.16220.059-0.18740.07730.18440.00520.7615-0.08070.10320.66570.04690.418830.414117.968-7.8196
20.26060.06030.0440.36760.13541.4757-0.01850.0778-0.0016-0.10410.0489-0.06530.00070.0010.00440.27480.01750.00050.20390.0260.382429.276825.229843.1277
30.4690.02410.25531.20420.36061.98550.0122-0.1577-0.02470.1276-0.04220.00520.1097-0.0230.00690.16390.0198-0.02740.18990.04250.308830.196825.020874.2821
40.0889-0.1240.68710.654-0.28061.8471-0.1351-0.15020.06120.18310.12430.0553-0.2577-0.21190.03450.3120.0853-0.02850.5246-0.03420.35627.911536.0389111.7553
50.397-0.2162-0.44540.09450.12941.6703-0.08970.50860.3555-0.10550.29930.4170.172-0.68-0.02060.8437-0.2092-0.08140.92250.13490.362827.192820.4234-6.3617
60.47850.08660.02520.4281-0.02031.1038-0.02020.00440.0465-0.12630.04-0.02240.050.00840.00980.27340.0156-0.00990.17170.00920.370328.489424.39243.235
71.28850.1163-0.32340.69570.0411.9952-0.0338-0.18340.05410.05180.012-0.0798-0.06450.05430.01980.19690.0261-0.02510.24360.01680.337931.514830.247673.6272
8-0.134-0.64240.67531.08740.32211.6377-0.1128-0.2510.02770.2550.13730.01030.0262-0.29580.00530.31050.045-0.04770.60660.00690.374928.167129.0892112.5703
90.01170.06610.09670.84870.87972.30110.47010.2061-0.49350.1624-0.1453-0.10340.44250.2608-0.01471.16020.12050.0730.8749-0.00360.788532.93212.3468-19.8512
100.0128-0.0182-0.13670.0130.21792.11320.02980.3464-0.0744-0.6980.20530.3020.5253-0.7312-0.01591.0019-0.0672-0.03030.5765-0.02310.314123.489618.28241.5604
110.92270.65420.47190.46850.19582.2117-0.06360.1584-0.0973-0.40090.1324-0.3556-0.06720.2619-0.00320.37340.01080.03440.2035-0.00830.359333.98424.209828.6359
120.87620.12810.38611.07080.10571.60860.0072-0.0239-0.0888-0.11440.03710.01170.0776-0.1772-0.0070.23270.00420.00160.16830.02560.356924.948123.773646.7212
130.57640.3140.57751.3361-0.19031.8365-0.0567-0.12540.10320.02780.0675-0.0521-0.004-0.27520.00110.12860.02680.01830.2060.01640.295924.833629.380965.0438
140.817-0.7941-0.33941.39980.03821.5734-0.0603-0.2147-0.1307-0.05310.2326-0.03630.4392-0.23660.0280.3257-0.0207-0.03290.21020.07660.373826.753211.902571.6399
150.65410.1808-0.18860.6820.65832.34070.017-0.1376-0.07210.0573-0.0652-0.0532-0.34840.1672-0.01050.2126-0.0041-0.04260.35060.03390.360632.660134.292886.7315
161.7183-0.16370.33171.47370.05312.1382-0.11740.20380.2680.25270.0901-0.1568-0.67330.510.00040.38940.0982-0.04350.5111-0.0090.421236.400232.7358124.431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 105 through 135 )A105 - 135
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 255 )A136 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 327 )A256 - 327
4X-RAY DIFFRACTION4chain 'A' and (resid 328 through 377 )A328 - 377
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 135 )B107 - 135
6X-RAY DIFFRACTION6chain 'B' and (resid 136 through 255 )B136 - 255
7X-RAY DIFFRACTION7chain 'B' and (resid 256 through 327 )B256 - 327
8X-RAY DIFFRACTION8chain 'B' and (resid 328 through 377 )B328 - 377
9X-RAY DIFFRACTION9chain 'C' and (resid 107 through 116 )C107 - 116
10X-RAY DIFFRACTION10chain 'C' and (resid 117 through 135 )C117 - 135
11X-RAY DIFFRACTION11chain 'C' and (resid 136 through 175 )C136 - 175
12X-RAY DIFFRACTION12chain 'C' and (resid 176 through 235 )C176 - 235
13X-RAY DIFFRACTION13chain 'C' and (resid 236 through 275 )C236 - 275
14X-RAY DIFFRACTION14chain 'C' and (resid 276 through 295 )C276 - 295
15X-RAY DIFFRACTION15chain 'C' and (resid 296 through 353 )C296 - 353
16X-RAY DIFFRACTION16chain 'C' and (resid 354 through 377 )C354 - 377

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