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- PDB-6frq: Structure of tetragonal Hen Egg-White Lysozyme co-crystallized in... -

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Basic information

Entry
Database: PDB / ID: 6frq
TitleStructure of tetragonal Hen Egg-White Lysozyme co-crystallized in presence of 100 mM Tb-Xo4 and 100 mM Potassium sodium tartrate tetrahydrate.
ComponentsLysozyme C
KeywordsHYDROLASE / nucleation / phasing / Tb-Xo4 / crystallophore
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / 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 - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TERBIUM(III) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.69 Å
AuthorsEngilberge, S. / Riobe, F. / Di Pietro, S. / Wagner, T. / Shima, S. / Girard, E. / Dumont, E. / Maury, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Chemistry / Year: 2018
Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.
Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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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)14,6844
Polymers14,3311
Non-polymers3533
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-17 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.700, 77.700, 38.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-413-

HOH

31A-419-

HOH

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Components

#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
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate pH 4.6, 800 mM sodium chloride, 100 mM sodium and potassium tartrate, 100 mM Tb-Xo4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.69→38.85 Å / Num. obs: 13611 / % possible obs: 99.58 % / Redundancy: 13.9 % / Biso Wilson estimate: 29.47 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.69→38.85 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.239 681 5 %RANDOM
Rwork0.201 ---
obs0.203 13610 99.5 %-
Displacement parametersBiso mean: 32.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.7799 Å20 Å20 Å2
2--2.7799 Å20 Å2
3----5.5597 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.69→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 122 1126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012019HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013618HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d434SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes309HARMONIC5
X-RAY DIFFRACTIONt_it2019HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion14.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2300SEMIHARMONIC4
LS refinement shellResolution: 1.69→1.82 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2386 136 5.01 %
Rwork0.2165 2578 -
all0.2176 2714 -
obs--98.4 %
Refinement TLS params.Method: refined / Origin x: -1.2345 Å / Origin y: 19.8178 Å / Origin z: 19.4047 Å
111213212223313233
T-0.0828 Å20.0073 Å2-0.0013 Å2--0.0638 Å2-0.0192 Å2--0.0447 Å2
L1.9141 °2-0.6875 °20.0343 °2-1.679 °2-0.1136 °2--0.8306 °2
S-0.0257 Å °0.0435 Å °-0.0445 Å °0.0889 Å °-0.0127 Å °0.1578 Å °-0.0085 Å °-0.0208 Å °0.0384 Å °
Refinement TLS groupSelection details: { A|* }

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