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- PDB-7cvl: Crystal structure of lysozyme by fixed-target serial synchrotron ... -

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Basic information

Entry
Database: PDB / ID: 7cvl
TitleCrystal structure of lysozyme by fixed-target serial synchrotron crystallography (500 ms)
ComponentsLysozyme C
KeywordsHYDROLASE / room temperature structure / serial crystallography / serial synchrotron crystallography
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: 1.6 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Crystals / Year: 2020
Title: Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder
Authors: Park, S.Y. / Choi, H. / Eo, C. / Cho, Y. / Nam, K.H.
History
DepositionAug 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)16,3524
Polymers16,2581
Non-polymers943
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.450, 79.450, 38.470
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-343-

HOH

21A-345-

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-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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 293.5 K / Method: small tubes / Details: sodium acetate, PEG 8000, NaCl

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.6→80 Å / Num. obs: 16824 / % possible obs: 100 % / Redundancy: 63.5 % / CC1/2: 0.9515 / CC star: 0.9875 / Net I/σ(I): 4.31
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 1627 / CC1/2: 0.568 / CC star: 0.8512
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: polyimide films / Sample holding: nylon-mesh

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JXQ

6jxq


Resolution: 1.6→56.18 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1679 10 %
Rwork0.1857 15106 -
obs0.1887 16785 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.23 Å2 / Biso mean: 28.1709 Å2 / Biso min: 12.84 Å2
Refinement stepCycle: final / Resolution: 1.6→56.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 81 1085
Biso mean--27.92 35.37 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.650.31651350.266412161351
1.65-1.70.26811380.247312421380
1.7-1.760.29641370.243812321369
1.76-1.830.26181380.209912411379
1.83-1.910.24181370.189712311368
1.92-2.020.21441380.174612461384
2.02-2.140.20381390.169912501389
2.14-2.310.19521380.158212451383
2.31-2.540.20871410.162712621403
2.54-2.910.21931400.172412651405
2.91-3.660.20121440.173912931437
3.66-56.180.20251540.201813831537

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