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- PDB-8fyg: Crystal structure of Hyaluronate lyase A from Cutibacterium acnes -

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Basic information

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


hyaluronate lyase / carbohydrate binding / carbohydrate metabolic process / lyase activity / 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 HL043PA1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionJan 26, 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

Downloads & links

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Assembly

Deposited unit
A: Hyaluronate lyase
B: Hyaluronate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6717
Polymers167,2402
Non-polymers4305
Water23,9961332
1
A: Hyaluronate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8664
Polymers83,6201
Non-polymers2463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hyaluronate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8043
Polymers83,6201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.960, 59.420, 125.990
Angle α, β, γ (deg.)90.61, 95.74, 90.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hyaluronate lyase


Mass: 83620.062 Da / Num. of mol.: 2 / Mutation: Y285F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes HL043PA1 (bacteria)
Strain: HL043PA1 / Gene: HMPREF9570_01449 / Plasmid: pET
Details (production host): pET His6 MBP TEV LIC cloning vector
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A828SH59, hyaluronate lyase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na dihydrogen phosphate pH 6.5, 9% PEG 8000, 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: Feb 20, 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: 2.05→19.8 Å / Num. obs: 88266 / % possible obs: 93.9 % / Redundancy: 2.2 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.128 / Net I/σ(I): 7.33
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.05-2.10.49761910.6230.6621
2.1-2.160.39764650.7540.5281
2.16-2.220.33961470.7660.4491
2.22-2.290.30260940.8240.4011
2.29-2.370.25458710.8770.3371
2.37-2.450.23357020.90.3081
2.45-2.540.20955270.9170.2761
2.54-2.650.16652870.9480.2191
2.65-2.760.14150540.9630.1871
2.76-2.90.12248740.9720.1611
2.9-3.060.10646060.9790.1391
3.06-3.240.08443320.9850.1111
3.24-3.470.07240310.9860.0961
3.47-3.740.05937290.9910.0781
3.74-4.10.05434230.9910.0721
4.1-4.580.05231320.990.0691
4.58-5.290.05127570.9920.0671
5.29-6.480.05323510.9910.071
6.48-9.170.04417980.9940.0581
9.17-19.80.0418950.9950.0541

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEVERSION Jun 1, 2017 BUILT=20170923data scaling
XDSVERSION Jun 1, 2017 BUILT=20170923data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.8 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 2006 2.27 %
Rwork0.2252 --
obs0.2259 88252 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11485 0 28 1332 12845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211773
X-RAY DIFFRACTIONf_angle_d0.54716090
X-RAY DIFFRACTIONf_dihedral_angle_d5.441644
X-RAY DIFFRACTIONf_chiral_restr0.0421865
X-RAY DIFFRACTIONf_plane_restr0.0092066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.351380.3195832X-RAY DIFFRACTION89
2.1-2.160.34271430.28436189X-RAY DIFFRACTION94
2.16-2.220.31811390.27346144X-RAY DIFFRACTION94
2.22-2.290.29941470.26836231X-RAY DIFFRACTION95
2.29-2.380.32261390.26036234X-RAY DIFFRACTION95
2.38-2.470.29881470.25736254X-RAY DIFFRACTION95
2.47-2.580.27541400.24776231X-RAY DIFFRACTION95
2.58-2.720.27981460.24036252X-RAY DIFFRACTION95
2.72-2.890.25421430.23426174X-RAY DIFFRACTION95
2.89-3.110.2511500.22756168X-RAY DIFFRACTION94
3.11-3.420.241430.21236183X-RAY DIFFRACTION94
3.42-3.910.25011480.19176077X-RAY DIFFRACTION93
3.91-4.920.19881400.17876121X-RAY DIFFRACTION93
4.92-19.80.21741430.20836156X-RAY DIFFRACTION94

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