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- PDB-4wg1: Room temperature crystal structure of lysozyme determined by seri... -

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Basic information

Entry
Database: PDB / ID: 4wg1
TitleRoom temperature crystal structure of lysozyme determined by serial synchrotron crystallography (micro focused beam - crystFEL)
ComponentsLysozyme C
KeywordsHYDROLASE / serial crystallography / serial synchrotron crystallography / crystFEL / nanopeakcell
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: 1.7 Å
AuthorsCoquelle, N. / Brewster, A.S. / Kapp, U. / Shilova, A. / Weimhausen, B. / Sauter, N.K. / Burghammer, M. / Colletier, J.P.
Funding support France, United States, 2items
OrganizationGrant numberCountry
Fondation France Alzheimer France
National Institutes of HealthGM102520 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams.
Authors: Coquelle, N. / Brewster, A.S. / Kapp, U. / Shilova, A. / Weinhausen, B. / Burghammer, M. / Colletier, J.P.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jul 27, 2016Group: Database references
Revision 1.4Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2932
Polymers16,2581
Non-polymers351
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.940, 77.940, 38.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 16257.660 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 50mM Sodium acetate pH 4.5, 16% PEG 4K, 3.5M NaCl / PH range: 4.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.954 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.7→55.1 Å / Num. obs: 13496 / % possible obs: 100 % / Redundancy: 114.8 % / Net I/σ(I): 3.4
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JLN

1jln


Resolution: 1.7→55.112 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 674 5 %
Rwork0.2261 --
obs0.2277 13477 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→55.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 84 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061077
X-RAY DIFFRACTIONf_angle_d0.8641457
X-RAY DIFFRACTIONf_dihedral_angle_d12.409389
X-RAY DIFFRACTIONf_chiral_restr0.038150
X-RAY DIFFRACTIONf_plane_restr0.003193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.83130.42651310.38142491X-RAY DIFFRACTION99
1.8313-2.01560.33281320.29682511X-RAY DIFFRACTION100
2.0156-2.30720.25931330.23682523X-RAY DIFFRACTION100
2.3072-2.90690.271350.2582570X-RAY DIFFRACTION100
2.9069-55.14090.22841430.19582708X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1032-0.02240.11290.4746-0.19850.1917-0.2479-0.2579-0.26180.62110.14110.0102-0.0288-0.5513-0.01340.3070.06860.06770.35850.03950.292115.6286-6.42628.533
20.8227-0.2398-0.15330.07670.10750.7075-0.18650.1392-0.3450.1006-0.03930.00990.3909-0.0285-0.00050.29730.00730.03110.2753-0.0040.311324.4052-6.750420.9949
30.10370.089-0.06710.2746-0.08760.024-0.05980.08150.29190.17440.26390.1604-0.2298-0.24070.00050.29330.0490.03410.33410.06510.348517.86059.959619.8178
40.04310.12630.02220.28930.08190.24560.1027-0.13090.1809-0.39880.07460.1413-0.10890.16740.00030.39430.07360.01140.3480.04020.3116.44146.834912.2204
50.0275-0.02750.06410.0314-0.07920.18920.38260.7640.142-0.5944-0.88390.8199-0.00910.3503-0.01820.45960.10640.00360.54590.03910.425513.93644.57665.1406
60.5371-0.44890.45540.4428-0.41380.32790.05860.42480.4527-0.29610.0216-0.12350.1096-0.0443-0.00040.3839-0.00670.01410.3393-0.00870.330417.7969-2.306614.6706
70.9727-0.62660.68760.6642-0.37130.50740.0540.82850.8322-0.5395-0.22080.2608-0.1390.59730.00380.4108-0.0340.00470.34680.02730.435431.19133.026420.1765
80.8690.4355-0.47381.3374-0.38020.5277-0.3741-0.2345-1.04630.23170.0919-0.8951-0.0019-0.1136-0.08020.36140.10080.0060.40850.12350.507528.1981-8.870530.5156
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 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 114 )
8X-RAY DIFFRACTION8chain 'A' and (resid 115 through 129 )

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