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- PDB-6fro: Crystal structure of Hen Egg-White Lysozyme co-crystallized in pr... -

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Basic information

Entry
Database: PDB / ID: 6fro
TitleCrystal structure of Hen Egg-White Lysozyme co-crystallized in presence of 100 mM Tb-Xo4 and 100 mM potassium iodide.
ComponentsLysozyme C
KeywordsHYDROLASE / nucleation / phasing / Tb-Xo4 / crystallophore
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
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
Tb-Xo4 / IODIDE ION / TERBIUM(III) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsEngilberge, S. / Riobe, F. / Di Pietro, 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 1.1May 29, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 17, 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

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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)15,7049
Polymers14,3311
Non-polymers1,3738
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-23 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.832, 78.832, 35.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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, 128 molecules

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


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Sodium acetate pH 4.6 100 mM, Sodium Chloride 800 mM, potassium iodide 100 mM. Tb-Xo4 was directly mixed with the protein solution at a final concentration of 100 mM prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.92356 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: 0.92356 Å / Relative weight: 1
ReflectionResolution: 1.42→39.41 Å / Num. obs: 21311 / % possible obs: 98.28 % / Redundancy: 14 % / Biso Wilson estimate: 18.72 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.029 / Net I/σ(I): 13.8
Reflection shellResolution: 1.42→1.49 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.916 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3031 / CC1/2: 0.75 / Rpim(I) all: 0.52 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H87

1h87


Resolution: 1.42→39.41 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1066 5 %RANDOM
Rwork0.257 ---
obs0.258 21312 98.6 %-
Displacement parametersBiso mean: 27.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.2561 Å20 Å20 Å2
2--0.2561 Å20 Å2
3----0.5122 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 1.42→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 36 120 1157
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093660HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d431SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes312HARMONIC5
X-RAY DIFFRACTIONt_it2046HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion14.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion132SEMIHARMONIC5
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_contact2382SEMIHARMONIC4
LS refinement shellResolution: 1.42→1.49 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.398 136 4.99 %
Rwork0.4087 2590 -
all0.4081 2726 -
obs--96.55 %
Refinement TLS params.Method: refined / Origin x: 0.4588 Å / Origin y: -20.4513 Å / Origin z: -0.3597 Å
111213212223313233
T-0.1437 Å20.0053 Å20.0049 Å2--0.1123 Å20.025 Å2--0.1065 Å2
L3.3398 °2-2.7435 °2-0.5024 °2-3.8081 °20.1738 °2--1.1584 °2
S0.0817 Å °0.0959 Å °0.7932 Å °-0.011 Å °-0.0873 Å °-0.6991 Å °-0.0452 Å °-0.0342 Å °0.0056 Å °
Refinement TLS groupSelection details: { A|* }

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