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- PDB-7ol8: Crystal structure of Lysozyme in complex with trifluoroethanol: o... -

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Basic information

Entry
Database: PDB / ID: 7ol8
TitleCrystal structure of Lysozyme in complex with trifluoroethanol: orthorhombic form
ComponentsLysozyme
KeywordsHYDROLASE / TFE complex
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cytolysis / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cytolysis / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme C / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
TRIFLUOROETHANOL / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsCamara-Artigas, A. / Salinas-Garcia, M.C. / Plaza-Garrido, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of Lysozyme in complex with TFE
Authors: Camara-Artigas, A. / Salinas-Garcia, M.C. / Plaza-Garrido, M.
History
DepositionMay 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6635
Polymers14,3311
Non-polymers3324
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-18 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.981, 54.867, 65.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.88 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.3M NaCl, 0.1M MES, 10mM NaH2PO4 plus 20% TFE in the reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976256 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 1.15→19.34 Å / Num. obs: 39025 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Rrim(I) all: 0.056 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.15-1.173.50.671641318230.6590.3970.785296.4
6.3-19.345.10.04214602840.9980.0190.04736.496.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F1O
Resolution: 1.15→19.34 Å / SU ML: 0.0979 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 18.4765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1823 3596 4.92 %
Rwork0.1545 69421 -
obs0.1559 39025 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.32 Å2
Refinement stepCycle: LAST / Resolution: 1.15→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 18 153 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01031050
X-RAY DIFFRACTIONf_angle_d1.011428
X-RAY DIFFRACTIONf_chiral_restr0.0778147
X-RAY DIFFRACTIONf_plane_restr0.0106187
X-RAY DIFFRACTIONf_dihedral_angle_d13.5534374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.170.26921400.26022398X-RAY DIFFRACTION89.9
1.17-1.180.27091650.24482593X-RAY DIFFRACTION96.77
1.18-1.20.21431770.21782700X-RAY DIFFRACTION98.97
1.2-1.220.26361250.20722653X-RAY DIFFRACTION99.39
1.22-1.230.25321150.19742691X-RAY DIFFRACTION99.29
1.23-1.260.21961180.18932767X-RAY DIFFRACTION99.14
1.26-1.280.22051420.18612648X-RAY DIFFRACTION99.25
1.28-1.30.20241560.16672675X-RAY DIFFRACTION99.02
1.3-1.320.21751310.15772662X-RAY DIFFRACTION98.94
1.32-1.350.17791320.16272728X-RAY DIFFRACTION99.06
1.35-1.380.16531580.14682659X-RAY DIFFRACTION99.51
1.38-1.410.20081090.1432728X-RAY DIFFRACTION98.92
1.41-1.450.17541280.14262689X-RAY DIFFRACTION99.12
1.45-1.490.21761210.13962709X-RAY DIFFRACTION98.99
1.49-1.530.16771280.1332684X-RAY DIFFRACTION98.98
1.53-1.580.18331430.13482688X-RAY DIFFRACTION99.12
1.58-1.640.14221320.13112680X-RAY DIFFRACTION99.01
1.64-1.70.16581520.12882664X-RAY DIFFRACTION99.19
1.7-1.780.19621490.13832682X-RAY DIFFRACTION99.12
1.78-1.870.16251440.1442687X-RAY DIFFRACTION98.92
1.87-1.990.15691670.14332650X-RAY DIFFRACTION98.46
1.99-2.150.17681470.13822667X-RAY DIFFRACTION98.98
2.15-2.360.17481390.13352664X-RAY DIFFRACTION99.26
2.36-2.70.21521350.15692672X-RAY DIFFRACTION98.11
2.7-3.40.12131330.17182681X-RAY DIFFRACTION98.77
3.4-19.340.21731100.15922702X-RAY DIFFRACTION98.53

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