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- PDB-6f2k: Crystal structure of Hen Egg-White Lysozyme co-crystallized in pr... -

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Basic information

Entry
Database: PDB / ID: 6f2k
TitleCrystal structure of Hen Egg-White Lysozyme co-crystallized in presence of 100 mM Tb-Xo4 and 100 mM potassium phosphate monobasic.
ComponentsLysozyme C
KeywordsHYDROLASE / Tb-Xo4 / crystallophore / nucleation / phasing
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEngilberge, S. / Riobe, F. / Di Pietro, S. / Girard, E. / Dumont, E. / Maury, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-01 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
DepositionNov 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5965
Polymers14,3311
Non-polymers2654
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-27 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.359, 78.359, 37.404
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-350-

HOH

21A-452-

HOH

31A-478-

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.: 1 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate pH 4.6, 200 to 800 sodium chloride, 100 mM Potassium phosphate monobasic. 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: 0.9797 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: 1.5→39.18 Å / Num. obs: 19187 / % possible obs: 98.22 % / Redundancy: 13.7 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Net I/σ(I): 19.16
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2702 / CC1/2: 0.819 / Rpim(I) all: 0.32 / % possible all: 98.6

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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: 1.5→35.04 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.24 944 5 %RANDOM
Rwork0.198 ---
obs0.2 18864 98.3 %-
Displacement parametersBiso mean: 23.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.7775 Å20 Å20 Å2
2---0.7775 Å20 Å2
3---1.555 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.5→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 4 194 1199
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012032HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.023642HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d437SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes313HARMONIC5
X-RAY DIFFRACTIONt_it2032HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.23
X-RAY DIFFRACTIONt_other_torsion14.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion135SEMIHARMONIC5
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_contact2453SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.59 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.224 151 5.02 %
Rwork0.1944 2855 -
all0.1959 3006 -
obs--99.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98341.30650.14170.7502-0.94021.5590.09590.2845-0.0192-0.1786-0.14490.25370.1445-0.05750.0490.10870.0423-0.0930.2042-0.09830.1159-6.627916.0459.4283
21.03210.25710.7380.80290.1921.2045-0.02690.0986-0.0620.20940.03730.31130.1494-0.0747-0.01040.07030.01220.02140.1876-0.04950.1243-11.618223.387820.5813
31.0671-0.3527-0.32961.4873-0.13291.0780.10090.1488-0.0262-0.0794-0.09210.0159-0.0506-0.0132-0.00880.08130.0349-0.0340.126-0.03080.04420.217321.699112.7985
40.95560.1617-0.91210.08830.4920.218-0.00550.0608-0.0252-0.0254-0.0425-0.1563-0.3936-0.24190.0480.113-0.0012-0.04210.1171-0.02110.079314.240119.579723.0608
50-0.5886-0.86610-0.63911.4662-0.14090.0763-0.14250.1130.16140.0049-0.275-0.1899-0.02050.08160.0273-0.02020.1214-0.02110.04995.546717.559320.3494
62.455-0.04050.70031.07790.07292.356-0.1165-0.2184-0.18720.1447-0.0140.14110.0894-0.07940.13040.10040.02520.00970.0976-0.00140.05454.852313.26527.4034
70.0026-0.1730.10410.3935-0.97620.4538-0.10030.0824-0.20440.23220.03590.30820.1422-0.12340.06440.07670.00150.01010.1203-0.02870.1076-5.328217.558124.8684
80.012-0.1429-0.35240.8257-0.78810.0002-0.0658-0.03050.05890.31630.0758-0.01510.12490.1961-0.010.1470.03250.00660.1511-0.01810.073-1.757327.994325.6142
90.5760.7939-0.01970.51310.72290.05750.0977-0.05-0.21020.0044-0.131-0.1138-0.18220.17390.03330.092-0.019-0.00310.1770.04360.1142.966931.509717.973
100.67590.8716-0.16510.08041.59121.4757-0.06910.16780.1039-0.129-0.05610.3297-0.1719-0.27380.12520.12820.0474-0.08030.22190.02340.1334-8.644328.37068.1307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|14 }
2X-RAY DIFFRACTION2{ A|15 - A|24 }
3X-RAY DIFFRACTION3{ A|25 - A|42 }
4X-RAY DIFFRACTION4{ A|43 - A|50 }
5X-RAY DIFFRACTION5{ A|51 - A|58 }
6X-RAY DIFFRACTION6{ A|59 - A|88 }
7X-RAY DIFFRACTION7{ A|89 - A|100 }
8X-RAY DIFFRACTION8{ A|101 - A|108 }
9X-RAY DIFFRACTION9{ A|109 - A|114 }
10X-RAY DIFFRACTION10{ A|115 - A|129 }

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