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- PDB-4zix: Structure of HEWL using Serial Femtosecond Crystallography of Sol... -

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Basic information

Entry
Database: PDB / ID: 4zix
TitleStructure of HEWL using Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsFromme, R. / Ishchenko, A. / Metz, M. / Roy-Chowdhury, S. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C.H. ...Fromme, R. / Ishchenko, A. / Metz, M. / Roy-Chowdhury, S. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C.H. / Weierstall, U. / Liu, W. / Cherezov, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108635 United States
CitationJournal: IUCrJ / Year: 2015
Title: Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase
Authors: Fromme, R. / Ishchenko, A. / Metz, M. / Roy-Chowdhury, S. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C.H. / Weierstall, U. / Liu, W. / Cherezov, V.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references / Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)14,4615
Polymers14,3311
Non-polymers1294
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.100, 79.100, 38.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-358-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 3.5
Details: Lysozyme powder from chicken egg white was dissolved in 0.02 M Sodium acetate pH 4.6 buffer to a final concentration of 50 mg/mL. Crystallization was initiated by injecting 20 uL of lysozyme ...Details: Lysozyme powder from chicken egg white was dissolved in 0.02 M Sodium acetate pH 4.6 buffer to a final concentration of 50 mg/mL. Crystallization was initiated by injecting 20 uL of lysozyme solution (50 mg/mL) into 1 mL of precipitant solution (20 %(w/v) NaCl, 6 %(v/v) PEG 6000, 1 M Na acetate pH 3.0) at room temperature.

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Data collection

DiffractionMean temperature: 273 K / Ambient temp details: Serial femtosecond crystallography
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.56 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 1.89→27.97 Å / Num. obs: 10266 / % possible obs: 100 % / Redundancy: 26558 % / Net I/σ(I): 9.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→27.966 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 520 5.07 %
Rwork0.1652 9746 -
obs0.1665 10266 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.29 Å2 / Biso mean: 32.7985 Å2 / Biso min: 15.92 Å2
Refinement stepCycle: final / Resolution: 1.89→27.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 4 89 1094
Biso mean--32.33 38.02 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031041
X-RAY DIFFRACTIONf_angle_d0.7131405
X-RAY DIFFRACTIONf_chiral_restr0.027146
X-RAY DIFFRACTIONf_plane_restr0.002185
X-RAY DIFFRACTIONf_dihedral_angle_d11.472375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8902-2.08040.20511290.192323742503
2.0804-2.38130.19071320.158423972529
2.3813-2.99960.20431220.178124142536
2.9996-27.96910.18231370.156925612698

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