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- PDB-7ac2: Structure of Hen Egg White Lysozyme collected by rotation serial ... -

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Basic information

Entry
Database: PDB / ID: 7ac2
TitleStructure of Hen Egg White Lysozyme collected by rotation serial crystallography on a COC membrane at a synchrotron source
ComponentsLysozyme
KeywordsHYDROLASE / hydrolyse
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
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-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.507 Å
AuthorsMartiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Vera, L. / Wang, M. / Marsh, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Versatile microporous polymer-based supports for serial macromolecular crystallography.
Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C.
History
DepositionSep 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4966
Polymers14,3311
Non-polymers1655
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-51 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.020, 79.020, 37.080
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-337-

HOH

21A-360-

HOH

31A-406-

HOH

41A-423-

HOH

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Components

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: batch mode
Details: dissolved 50 mg/ml in 100 mM Na Acetate pH 3.0. mixed 1:1 (v:v) with 19.04% NaCl, 5.44% PEG 8000, 68 mM Na acetate pH 3.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→39.51 Å / Num. obs: 19098 / % possible obs: 99.7 % / Redundancy: 26.5 % / CC1/2: 0.997 / Net I/σ(I): 10.44
Reflection shellResolution: 1.5→1.54 Å / Mean I/σ(I) obs: 0.44 / Num. unique obs: 1880 / CC1/2: 0.172
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: COC thin membrane

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NE0

5ne0


Resolution: 1.507→39.51 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 949 5 %
Rwork0.1801 18027 -
obs0.1815 18976 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.36 Å2 / Biso mean: 31.473 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 1.507→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 6 125 1122
Biso mean--33.41 39.84 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5073-1.58680.32491270.3049242595
1.5868-1.68620.29661340.27222545100
1.6862-1.81640.29391340.22362535100
1.8164-1.99910.22781350.18232568100
1.9991-2.28840.18291350.16292575100
2.2884-2.8830.211380.18662617100
2.883-39.510.19411460.16542762100
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)
16.1027-2.43571.25192.6513-1.19284.8215-0.010.3360.3128-0.19290.0101-0.3796-0.39750.26360.0040.2626-0.04970.06620.25150.00450.31186.5993-16.6003-9.26
25.66780.71740.94159.19131.55961.2016-0.2401-0.0581-0.17990.01810.525-1.09590.05750.4049-0.21910.21220.0161-0.0310.3365-0.03580.314111.3977-23.64281.7878
32.1946-1.1677-0.06052.38630.07342.0199-0.00310.0973-0.06190.2078-0.03290.10220.0991-0.20670.03440.2142-0.01320.01410.1879-0.00110.206-4.7477-21.3312-2.6997
44.5427-1.49260.90935.12541.52465.3258-0.203-0.2632-0.07630.280.16050.40340.39360.05570.07290.25690.02640.02190.2310.00850.2358-7.2345-16.94786.9211
53.1247-1.6270.3622.46830.42161.1475-0.1517-0.2410.34880.17210.1606-0.2088-0.11480.0261-0.00130.23650.0086-0.0160.2409-0.0260.2696-0.4391-14.10347.0464
67.35010.43093.74865.76480.64898.6572-0.0643-0.4557-0.25480.63840.06230.18440.3085-0.86860.08250.21580.00150.03680.2605-0.0020.2391-0.1851-29.75173.7585
75.2552.5362-4.73696.181-5.21478.7234-0.041-0.1295-0.1726-0.3439-0.1456-0.65410.14990.64460.1560.26270.01050.03020.3227-0.04940.28378.0508-28.903-10.0267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )A15 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 50 )A25 - 50
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 68 )A51 - 68
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 99 )A69 - 99
6X-RAY DIFFRACTION6chain 'A' and (resid 100 through 114 )A100 - 114
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 129 )A115 - 129

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