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- PDB-6f9x: Lysozyme crystallized in presence of 100 mM lithium sulphate at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 6f9x
TitleLysozyme crystallized in presence of 100 mM lithium 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: 1.25 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 6, 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)14,2284
Polymers14,0611
Non-polymers1673
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-33 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.090, 56.214, 73.134
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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 44.08 % / Mosaicity: 0.15 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM Lithium Sulphate, 0.3 M Sodium Chloride, 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: 1.25→19.77 Å / Num. obs: 30557 / % possible obs: 86.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.028 / Rrim(I) all: 0.064 / Net I/σ(I): 12.8 / Num. measured all: 155400 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.274.80.57736307520.8490.2820.6452.345.2
6.85-19.774.60.03811622550.9940.020.04328.395.6

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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: 1.25→19.775 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 2898 5.1 %
Rwork0.1654 53894 -
obs0.1669 56792 85.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.69 Å2 / Biso mean: 18.0392 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 1.25→19.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 7 126 1110
Biso mean--32.97 26.27 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081045
X-RAY DIFFRACTIONf_angle_d0.8791424
X-RAY DIFFRACTIONf_chiral_restr0.072148
X-RAY DIFFRACTIONf_plane_restr0.005185
X-RAY DIFFRACTIONf_dihedral_angle_d19.439387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.27050.2481550.22141193124841
1.2705-1.29240.27141390.22123001314099
1.2924-1.31590.29341750.22412953312898
1.3159-1.34120.2441800.21572889306999
1.3412-1.36860.29931540.2212975312998
1.3686-1.39830.25851460.21322888303497
1.3983-1.43080.22791640.17782966313098
1.4308-1.46660.2129840.18031842192662
1.4666-1.50630.18021280.14872145227396
1.5063-1.55060.1911030.14792150225372
1.5506-1.60060.19211420.150829933135100
1.6006-1.65780.21731690.153729863155100
1.6578-1.72410.21481000.15482622272298
1.7241-1.80250.21861510.15982802295398
1.8025-1.89750.1761480.15532623277187
1.8975-2.01630.1706930.16551596168953
2.0163-2.17180.20441130.15392409252281
2.1718-2.390.2081380.1562537267585
2.39-2.7350.19211810.17342743292492
2.735-3.44290.20251760.16392871304798
3.4429-19.77730.14641590.1562710286992

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