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- PDB-8g0o: Crystal structure of Y281F mutant of Hyaluronate lyase B from Cut... -

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Basic information

Entry
Database: PDB / ID: 8g0o
TitleCrystal structure of Y281F mutant of Hyaluronate lyase B from Cutibacterium acnes
ComponentsHyaluronate lyase
KeywordsLYASE / Polysaccharide lyase / Glycosaminoglycan (GAG) lyase / Hyaluronate lyase / Inflammation
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Glycoside hydrolase-type carbohydrate-binding ...Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Biological speciesCutibacterium acnes HL110PA3 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKatiki, M. / McNally, R. / Chatterjee, A. / Hajam, I.A. / Liu, G.Y. / Murali, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI141401 United States
CitationJournal: Nat Commun / Year: 2023
Title: Functional divergence of a bacterial enzyme promotes healthy or acneic skin.
Authors: Hajam, I.A. / Katiki, M. / McNally, R. / Lazaro-Diez, M. / Kolar, S. / Chatterjee, A. / Gonzalez, C. / Paulchakrabarti, M. / Choudhury, B. / Caldera, J.R. / Desmond, T. / Tsai, C.M. / Du, X. ...Authors: Hajam, I.A. / Katiki, M. / McNally, R. / Lazaro-Diez, M. / Kolar, S. / Chatterjee, A. / Gonzalez, C. / Paulchakrabarti, M. / Choudhury, B. / Caldera, J.R. / Desmond, T. / Tsai, C.M. / Du, X. / Li, H. / Murali, R. / Liu, G.Y.
History
DepositionFeb 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyaluronate lyase
B: Hyaluronate lyase


Theoretical massNumber of molelcules
Total (without water)166,9262
Polymers166,9262
Non-polymers00
Water12,034668
1
A: Hyaluronate lyase


Theoretical massNumber of molelcules
Total (without water)83,4631
Polymers83,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hyaluronate lyase


Theoretical massNumber of molelcules
Total (without water)83,4631
Polymers83,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.977, 53.013, 161.016
Angle α, β, γ (deg.)91.95, 98.03, 114.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hyaluronate lyase / Hyaluronidase / HYase


Mass: 83462.992 Da / Num. of mol.: 2 / Mutation: Y281F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes HL110PA3 (bacteria)
Strain: HL110PA3 / Gene: PPA0380 / Plasmid: pET / Details (production host): pET His6 TEV LIC cloning vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CZ01, hyaluronate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M bis-tris pH 6.5, 0.4 M MgCl2, 16% PEG 3350, and 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2018
RadiationMonochromator: MSC/Yale double focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→19.72 Å / Num. obs: 85175 / % possible obs: 92.5 % / Redundancy: 1.9 % / CC1/2: 0.981 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.12 / Rrim(I) all: 0.17 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.548 / Num. unique obs: 11885 / CC1/2: 0.853 / Rpim(I) all: 0.548 / Rrim(I) all: 0.775

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALA3.3.21data scaling
XDSVERSION Nov 1, 2016 BUILT=20170215data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.72 Å / Cross valid method: FREE R-VALUE / σ(F): 16.43 / Phase error: 42.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2741 4357 5.12 %
Rwork0.2436 --
obs0.271 85171 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11563 0 0 668 12231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311831
X-RAY DIFFRACTIONf_angle_d0.54316140
X-RAY DIFFRACTIONf_dihedral_angle_d4.4341660
X-RAY DIFFRACTIONf_chiral_restr0.0411832
X-RAY DIFFRACTIONf_plane_restr0.0042089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.3662080.3263530X-RAY DIFFRACTION76
2.13-2.170.36482180.3193919X-RAY DIFFRACTION86
2.17-2.210.36062380.31464062X-RAY DIFFRACTION87
2.21-2.260.37662150.32033919X-RAY DIFFRACTION87
2.26-2.310.36512340.31284148X-RAY DIFFRACTION88
2.31-2.360.36671930.30883974X-RAY DIFFRACTION88
2.36-2.420.31492220.32374086X-RAY DIFFRACTION88
2.42-2.490.39782020.31324091X-RAY DIFFRACTION89
2.49-2.560.34351880.30684059X-RAY DIFFRACTION90
2.56-2.640.35742230.30954145X-RAY DIFFRACTION89
2.64-2.730.35822000.30064090X-RAY DIFFRACTION90
2.73-2.840.35731730.2954198X-RAY DIFFRACTION91
2.84-2.970.34971830.28584140X-RAY DIFFRACTION91
2.97-3.130.32311960.27794203X-RAY DIFFRACTION91
3.13-3.320.32972180.2584158X-RAY DIFFRACTION90
3.32-3.580.29531930.24884136X-RAY DIFFRACTION90
3.58-3.940.22441970.22844047X-RAY DIFFRACTION89
3.94-4.50.21731800.21214087X-RAY DIFFRACTION88
4.5-5.650.22532080.22094029X-RAY DIFFRACTION88
5.65-19.720.25221660.23624095X-RAY DIFFRACTION89

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