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- PDB-6f1m: Lysozyme crystallized in presence of 100 mM sodium phosphate at p... -

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Basic information

Entry
Database: PDB / ID: 6f1m
TitleLysozyme crystallized in presence of 100 mM sodium phosphate at pH 4.5: low-humidity form
ComponentsLysozyme C
KeywordsHYDROLASE
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding.
Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A.
History
DepositionNov 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.104, 55.522, 66.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1.96 Å3/Da / Density % sol: 37.3 % / Mosaicity: 0.54 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.5 M Sodium Chloride, 0.1 M Sodium Phosphate. 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationMonochromator: CHANNEL-CUT MONOCHROMATOR AND A KIRKPATRICK-BAEZ (KB) FOCUSING SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.48→19.5 Å / Num. obs: 17334 / % possible obs: 90.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.57 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.043 / Rrim(I) all: 0.102 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.48-1.54.60.5279330.6640.2660.59598.3
8.09-19.54.80.0551170.9930.0260.06183

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E3U

4e3u


Resolution: 1.48→19.497 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.29 / Phase error: 24.35
RfactorNum. reflection% reflection
Rfree0.2584 1521 4.87 %
Rwork0.2259 --
obs0.2275 17311 86.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.8 Å2 / Biso mean: 21.6305 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 1.48→19.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 72 1026
Biso mean---23.48 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008978
X-RAY DIFFRACTIONf_angle_d0.9921329
X-RAY DIFFRACTIONf_chiral_restr0.071141
X-RAY DIFFRACTIONf_plane_restr0.006171
X-RAY DIFFRACTIONf_dihedral_angle_d18.162346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4768-1.52450.35971630.30582907307093
1.5245-1.57890.32561590.27632928308794
1.5789-1.64210.3051530.25762892304594
1.6421-1.71680.27141360.23732870300693
1.7168-1.80720.25371290.23312860298992
1.8072-1.92040.24321710.23442792296391
1.9204-2.06850.2576940.22651927202166
2.0685-2.27640.28261230.22922279240277
2.2764-2.60510.26731550.21782846300192
2.6051-3.27960.24961050.22852639274484
3.2796-19.49910.22171330.20032749288289

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