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- PDB-6wwx: Crystal structure of truncated bacteriophage hyaluronan lyase Hyl... -

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Basic information

Entry
Database: PDB / ID: 6wwx
TitleCrystal structure of truncated bacteriophage hyaluronan lyase HylP in complex with unsaturated hyaluronan tetra-saccharides
ComponentsHyaluronoglucosaminidase
KeywordsLYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination
Function / homology
Function and homology information


hyaluronoglucosaminidase / symbiont entry into host cell via disruption of host cell glycocalyx / 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: 2.2 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 9, 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: Hyaluronoglucosaminidase
B: Hyaluronoglucosaminidase
C: Hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20810
Polymers94,5973
Non-polymers4,6107
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62490 Å2
ΔGint-134 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.535, 86.819, 168.646
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
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA107 - 37621 - 290
21ASNASNBB107 - 37621 - 290
12THRTHRAA106 - 37620 - 290
22THRTHRCC106 - 37620 - 290
13ASNASNBB107 - 37621 - 290
23ASNASNCC107 - 37621 - 290

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Hyaluronoglucosaminidase / Hyaluronidase / 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, hyaluronoglucosaminidase
#2: Polysaccharide
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 758.633 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-3/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-4-deoxy-GlcpA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356
Source method: isolated from a genetically manipulated 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: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% (v/v) 2-Propanol, 20% (w/v) PEG 4000, 0.1 M Hepes, pH 7.5; incubation of protein HylP with unsaturated Hyaluronan tetra-saccharides at 1:20 molar ratio prior to crystallization

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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: May 29, 2012
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: 51169 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.325 / Net I/av σ(I): 30.4 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 5022 / Χ2: 1.185 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WV2

6wv2


Resolution: 2.2→38.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.337 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 2595 5.1 %RANDOM
Rwork0.1824 ---
obs0.1839 48493 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.38 Å2 / Biso mean: 44.9 Å2 / Biso min: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.2→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 313 356 6771
Biso mean--52.71 44.27 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196517
X-RAY DIFFRACTIONr_bond_other_d0.0020.026080
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.958733
X-RAY DIFFRACTIONr_angle_other_deg0.893314259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84126.245237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.876151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0181515
X-RAY DIFFRACTIONr_chiral_restr0.0720.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A127480.08
12B127480.08
21A127640.07
22C127640.07
31B127000.08
32C127000.08
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.273 192 -
Rwork0.249 3393 -
obs--96.4 %
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)
10.1107-0.04870.18750.15220.1921.33030.0082-0.07410.0284-0.05950.0461-0.03020.0321-0.0434-0.05430.07010.0101-0.01080.0649-0.02270.026429.498526.86858.2051
20.1369-0.020.10640.11490.1751.2405-0.0095-0.08370.0277-0.0610.0321-0.01690.0485-0.0256-0.02270.07850.0059-0.01250.0582-0.02380.027829.19926.694558.8644
30.0611-0.03640.13980.18070.141.3608-0.0036-0.06470.012-0.06770.0557-0.0250.0262-0.0201-0.05210.05980.0173-0.00820.0853-0.02210.017229.588226.4458.4253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A105 - 175
2X-RAY DIFFRACTION1A176 - 255
3X-RAY DIFFRACTION1A256 - 327
4X-RAY DIFFRACTION1A328 - 377
5X-RAY DIFFRACTION2B107 - 134
6X-RAY DIFFRACTION2B135 - 194
7X-RAY DIFFRACTION2B195 - 234
8X-RAY DIFFRACTION2B235 - 274
9X-RAY DIFFRACTION2B275 - 294
10X-RAY DIFFRACTION2B295 - 353
11X-RAY DIFFRACTION2B354 - 377
12X-RAY DIFFRACTION3C106 - 135
13X-RAY DIFFRACTION3C136 - 175
14X-RAY DIFFRACTION3C176 - 235
15X-RAY DIFFRACTION3C236 - 353
16X-RAY DIFFRACTION3C354 - 377

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