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- PDB-6wxa: Crystal structure of truncated Streptococcal bacteriophage hyalur... -

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Basic information

Entry
Database: PDB / ID: 6wxa
TitleCrystal structure of truncated Streptococcal bacteriophage hyaluronidase complexed with unsaturated hyaluronan hexa-saccharides
ComponentsHyaluronan lyase
KeywordsLYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination / unsaturated Hyaluronan hexa-saccharides
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: 2.3 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 10, 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)99,4299
Polymers94,5973
Non-polymers4,8326
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area63040 Å2
ΔGint-140 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.296, 86.492, 168.226
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
11LYSLYSAA103 - 37617 - 290
21LYSLYSBB103 - 37617 - 290
12GLUGLUAA104 - 37618 - 290
22GLUGLUCC104 - 37618 - 290
13GLUGLUBB104 - 37618 - 290
23GLUGLUCC104 - 37618 - 290

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Sugars , 3 types, 5 molecules

#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-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1137.950 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-2-1-3/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-4-deoxy-IdopA]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic 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: 979.841 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5]/1-2-1-2-1/a3-b1_b4-c1_c3-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#4: 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.: 2
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

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Non-polymers , 2 types, 139 molecules

#5: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

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, 20% (w/v) PEG 4000, 0.1M HEPES PH 7.5; Addition of unsaturated Hyaluronan Hexa-saccharides 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: 2.3→50 Å / Num. obs: 44512 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.573 / Net I/av σ(I): 29 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4399 / Χ2: 1.345 / % possible all: 100

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Processing

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

6wv2


Resolution: 2.3→44.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.233 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.33 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2231 5 %RANDOM
Rwork0.2098 ---
obs-42152 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.4 Å2 / Biso mean: 52.3 Å2 / Biso min: 28.66 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å2-0 Å20 Å2
2--2.17 Å2-0 Å2
3---2.15 Å2
Refinement stepCycle: final / Resolution: 2.3→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 328 138 6648
Biso mean--57.11 46.59 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196625
X-RAY DIFFRACTIONr_bond_other_d0.0030.026168
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.958875
X-RAY DIFFRACTIONr_angle_other_deg0.969314473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4926.311244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.865151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8161515
X-RAY DIFFRACTIONr_chiral_restr0.0920.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027162
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021099
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128880.08
12B128880.08
21A128040.09
22C128040.09
31B128660.08
32C128660.08
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 236 -
Rwork0.338 4091 -
obs--98.56 %
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)
10.0707-0.02140.25880.13730.09221.46660.012-0.04640.0111-0.08090.0171-0.03690.0423-0.0942-0.02920.36250.0176-0.02040.0477-0.0150.016629.230226.360757.085
20.0801-0.01660.09670.13210.14551.41550.0014-0.06150.0151-0.07740.0023-0.01510.0622-0.0507-0.00370.37610.0174-0.02750.0495-0.01160.007828.913726.027557.3395
30.0586-0.02770.1460.11840.04371.3090.0141-0.05790.0012-0.08660.0323-0.01520.022-0.0557-0.04650.3640.0159-0.02390.0681-0.00810.00729.424925.993457.8393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A102 - 116
2X-RAY DIFFRACTION1A117 - 174
3X-RAY DIFFRACTION1A175 - 194
4X-RAY DIFFRACTION1A195 - 234
5X-RAY DIFFRACTION1A235 - 254
6X-RAY DIFFRACTION1A255 - 294
7X-RAY DIFFRACTION1A295 - 353
8X-RAY DIFFRACTION1A354 - 377
9X-RAY DIFFRACTION2B103 - 116
10X-RAY DIFFRACTION2B117 - 134
11X-RAY DIFFRACTION2B135 - 174
12X-RAY DIFFRACTION2B175 - 194
13X-RAY DIFFRACTION2B195 - 214
14X-RAY DIFFRACTION2B215 - 234
15X-RAY DIFFRACTION2B235 - 274
16X-RAY DIFFRACTION2B275 - 294
17X-RAY DIFFRACTION2B295 - 327
18X-RAY DIFFRACTION2B328 - 353
19X-RAY DIFFRACTION2B354 - 377
20X-RAY DIFFRACTION3C104 - 175
21X-RAY DIFFRACTION3C176 - 235
22X-RAY DIFFRACTION3C236 - 353
23X-RAY DIFFRACTION3C354 - 377

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