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- PDB-5f16: CTA-modified hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 5f16
TitleCTA-modified hen egg-white lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme
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 / Resolution: 1.2 Å
AuthorsMcGlone, C. / Nix, J.C. / Page, R.C.
CitationJournal: Biomacromolecules / Year: 2016
Title: Investigating the Impact of Polymer Functional Groups on the Stability and Activity of Lysozyme-Polymer Conjugates.
Authors: Lucius, M. / Falatach, R. / McGlone, C. / Makaroff, K. / Danielson, A. / Williams, C. / Nix, J.C. / Konkolewicz, D. / Page, R.C. / Berberich, J.A.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-40 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.111, 78.111, 37.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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) / Tissue: egg-white / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 143 / 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: 38.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2M sodium chloride, 12% (w/v) PEG 6000 / PH range: 7.3-7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→55.233 Å / Num. obs: 36732 / % possible obs: 99.3 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.9
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.337 / Mean I/σ(I) obs: 1.6 / Num. unique all: 5278 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F14
Resolution: 1.2→55.233 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1938 5.46 %Random selection
Rwork0.2088 ---
obs0.211 35488 95.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→55.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 4 143 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061051
X-RAY DIFFRACTIONf_angle_d0.9891425
X-RAY DIFFRACTIONf_dihedral_angle_d12.22381
X-RAY DIFFRACTIONf_chiral_restr0.041150
X-RAY DIFFRACTIONf_plane_restr0.004188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22960.56731230.55432092X-RAY DIFFRACTION86
1.2296-1.26290.52311310.49012309X-RAY DIFFRACTION94
1.2629-1.30010.53131290.51562176X-RAY DIFFRACTION89
1.3001-1.3420.33681310.30342271X-RAY DIFFRACTION92
1.342-1.390.3251400.29642451X-RAY DIFFRACTION100
1.39-1.44570.23351430.22572468X-RAY DIFFRACTION100
1.4457-1.51150.27281370.26122386X-RAY DIFFRACTION97
1.5115-1.59110.25741410.20212484X-RAY DIFFRACTION100
1.5911-1.69080.22571440.17542482X-RAY DIFFRACTION100
1.6908-1.82140.20481440.18022494X-RAY DIFFRACTION100
1.8214-2.00470.23211440.20512462X-RAY DIFFRACTION98
2.0047-2.29480.19311430.17332489X-RAY DIFFRACTION99
2.2948-2.89120.21821470.16832561X-RAY DIFFRACTION100
2.8912-55.29140.22991410.16772425X-RAY DIFFRACTION90
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1680.7876-1.13283.8373-0.26471.241-0.43830.1983-0.5041-0.60790.1782-0.49050.35280.02010.07460.2704-0.02020.10680.1363-0.07850.2878-16.195-7.0248-18.5667
23.93860.24343.02997.1798-0.4582.78370.078-0.0918-0.6959-0.0609-0.0361-0.07460.3951-0.0634-0.0810.2425-0.01620.06060.11420.02390.2444-23.4766-12.1146-7.8133
34.68952.0721-0.92612.1901-0.99630.9551-0.15110.1108-0.0029-0.18480.1054-0.05180.0867-0.08990.0350.1488-0.02040.01580.1043-0.03510.1345-21.55350.0831-15.3024
45.1046-1.5129-1.60145.17060.19755.77520.0362-0.20320.2344-0.1298-0.06630.0288-0.0387-0.42350.00310.0824-0.00090.00190.102-0.0270.1159-18.37059.344-6.4919
53.57093.98050.0218.6724-1.76274.47310.0576-0.55930.51040.5133-0.19610.1192-0.0075-0.35560.01380.11190.0020.0020.1947-0.05440.155-15.77638.0011.3332
67.2663-1.6635-1.94514.61624.27254.1024-0.1332-0.8382-0.12960.608-0.12490.04790.2692-0.13560.24180.17310.0011-0.00810.25070.01510.1129-13.87354.84654.7823
72.83332.77372.72988.78215.78656.9053-0.09610.1334-0.3315-0.07860.0886-0.34330.26610.2498-0.00720.10370.02180.04230.11120.01140.1919-9.24531.0132-9.0778
86.0727-0.5619-4.7515.56120.96593.9978-0.1157-0.4627-0.48420.198-0.0203-0.16280.3280.04370.17470.1615-0.00550.00140.1480.03390.1929-17.4886-5.3887-3.2141
97.3899-2.8964.70737.1273-6.06146.7842-0.2399-0.50420.23670.34630.08370.029-0.5597-0.35660.1140.1640.00580.00860.1249-0.02160.1371-29.58090.3109-6.2367
106.6968-5.3869-4.53375.9954.85164.0201-0.11590.5333-0.6941-0.2303-0.19650.290.4558-0.41750.36530.2937-0.0686-0.00530.1736-0.05640.2188-28.3307-8.842-20.0156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 58 )
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 88 )
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 100 )
9X-RAY DIFFRACTION9chain 'A' and (resid 101 through 114 )
10X-RAY DIFFRACTION10chain 'A' and (resid 115 through 129 )

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