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- PDB-6fa0: Lysozyme crystallized in presence of 100 mM ammonium sulphate at ... -

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Basic information

Entry
Database: PDB / ID: 6fa0
TitleLysozyme crystallized in presence of 100 mM ammonium sulphate at pH 4.5
ComponentsLysozyme C
KeywordsHYDROLASE
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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
DepositionDec 15, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,1923
Polymers14,0611
Non-polymers1322
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-21 kcal/mol
Surface area6350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.088, 56.282, 73.208
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: 14060.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.2 % / Mosaicity: 0.23 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM Ammonium Sulphate, 0.4 M Sodium Chloride, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2017 / Details: Compound Refractive Lens
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.3→19.79 Å / Num. obs: 28509 / % possible obs: 91 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.024 / Rrim(I) all: 0.054 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.3-1.324.60.69715040.7470.3590.78899.6
7.12-19.794.10.0352200.9990.0180.03994.2

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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: 1.3→19.788 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 17.18
RfactorNum. reflection% reflection
Rfree0.1876 2562 4.91 %
Rwork0.1512 --
obs0.153 28443 88.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.16 Å2 / Biso mean: 18.981 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.3→19.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 6 172 1159
Biso mean--27.7 28.17 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071046
X-RAY DIFFRACTIONf_angle_d0.8841425
X-RAY DIFFRACTIONf_chiral_restr0.074147
X-RAY DIFFRACTIONf_plane_restr0.005186
X-RAY DIFFRACTIONf_dihedral_angle_d19.192390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3001-1.32510.25671660.24183024319098
1.3251-1.35210.21761510.20973115326699
1.3521-1.38150.29421390.25132997313695
1.3815-1.41360.22141630.18353073323699
1.4136-1.4490.23581870.17993051323898
1.449-1.48810.2406960.16521963205963
1.4881-1.53190.20241180.14452012213065
1.5319-1.58130.21151390.13023098323797
1.5813-1.63780.17151550.12043037319298
1.6378-1.70340.14041880.11973049323798
1.7034-1.78080.2141270.12392389251677
1.7808-1.87470.19341430.12813080322397
1.8747-1.9920.1978920.13552218231071
1.992-2.14570.16361090.13552424253377
2.1457-2.36130.14491180.14042365248376
2.3613-2.70220.18781650.14922946311195
2.7022-3.40170.17631490.15643032318197
3.4017-19.78980.19191570.15852795295290

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