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- PDB-6tvy: Structure of hen egg white lysozyme crystallized in the presence ... -

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Basic information

Entry
Database: PDB / ID: 6tvy
TitleStructure of hen egg white lysozyme crystallized in the presence of Tb-Xo4 crystallophore in the XtalController device
ComponentsLysozyme C
KeywordsANTIMICROBIAL PROTEIN / Glycosidase / Hydrolase / beta-N-acetylglucosaminidase
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
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
Tb-Xo4 / TERBIUM(III) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
Authorsde Wijn, R. / Rollet, K. / Coudray, L. / McEwen, A.G. / Lorber, B. / Sauter, C.
Funding support France, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-0036_NETRNA France
French National Research AgencyANR-11-LABX-0057_MITOCROSS France
French National Research AgencyANR-10-LABX-0036_INRT France
French National Research AgencyANR-13-BS07-0007-01 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05 France
CitationJournal: Crystals / Year: 2020
Title: Monitoring the Production of High Diffraction-Quality Crystals of Two Enzymes in Real Time Using In Situ Dynamic Light Scattering
Authors: de Wijn, R. / Rollet, K. / Engilberge, S. / McEwen, A.G. / Hennig, O. / Betat, H. / Moerl, M. / Riobe, F. / Maury, O. / Girard, E. / Benas, P. / Lorber, B. / Sauter, C.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2997
Polymers14,3311
Non-polymers9686
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-44 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.810, 78.810, 38.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4Tb / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.8 % / Description: Classical prismatic HEWL crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Lysozyme stock solution at 50 mg/ml in 10 mM Sodium Acetate pH 4.5, 40 mM NaCl, incubated in the XtalController instrument. The crystallization was triggered by the addition of 10mM Tb-Xo4 crystallophore.
Temp details: +/_ 0.1

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.51→35.24 Å / Num. obs: 36571 / % possible obs: 99.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 1 / Rrim(I) all: 0.036 / Net I/σ(I): 29.7
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5936 / CC1/2: 0.78 / Rrim(I) all: 0.726 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f2i

6f2i


Resolution: 1.51→35.24 Å / SU ML: 0.1635 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9551
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1749 3639 10.03 %
Rwork0.1415 32652 -
obs0.145 36291 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.11 Å2
Refinement stepCycle: LAST / Resolution: 1.51→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 35 54 1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441052
X-RAY DIFFRACTIONf_angle_d0.7121422
X-RAY DIFFRACTIONf_chiral_restr0.0461144
X-RAY DIFFRACTIONf_plane_restr0.0039185
X-RAY DIFFRACTIONf_dihedral_angle_d13.0215381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.3061220.2691142X-RAY DIFFRACTION88.58
1.53-1.550.29881340.25041239X-RAY DIFFRACTION97.72
1.55-1.570.26911440.23491264X-RAY DIFFRACTION99.58
1.57-1.590.27471370.19991253X-RAY DIFFRACTION99.5
1.59-1.620.25721330.1921261X-RAY DIFFRACTION99.43
1.62-1.640.20951400.16441251X-RAY DIFFRACTION99.29
1.64-1.670.23131430.15391265X-RAY DIFFRACTION98.74
1.67-1.70.1881380.15651215X-RAY DIFFRACTION98.83
1.7-1.730.191410.15211266X-RAY DIFFRACTION99.36
1.73-1.770.21921380.14271244X-RAY DIFFRACTION99.64
1.77-1.810.1771400.14071271X-RAY DIFFRACTION99.86
1.81-1.850.20981450.14071262X-RAY DIFFRACTION100
1.85-1.90.18761440.11721278X-RAY DIFFRACTION99.93
1.9-1.950.16121430.11341253X-RAY DIFFRACTION100
1.95-2.010.16111460.11511279X-RAY DIFFRACTION100
2.01-2.070.191390.12481259X-RAY DIFFRACTION99.93
2.07-2.140.15641390.11991274X-RAY DIFFRACTION100
2.14-2.230.15461390.1321256X-RAY DIFFRACTION100
2.23-2.330.16931420.12571256X-RAY DIFFRACTION100
2.33-2.450.16461440.13821271X-RAY DIFFRACTION100
2.45-2.610.18141420.14451259X-RAY DIFFRACTION100
2.61-2.810.19711450.15321269X-RAY DIFFRACTION100
2.81-3.090.17641380.16011255X-RAY DIFFRACTION100
3.09-3.540.17171390.14721276X-RAY DIFFRACTION100
3.54-4.460.15911390.12131258X-RAY DIFFRACTION100
4.46-35.240.1491450.14191276X-RAY DIFFRACTION100

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