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- PDB-7bvm: Crystal structure of lysozyme delivered in wheat starch -

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Basic information

Entry
Database: PDB / ID: 7bvm
TitleCrystal structure of lysozyme delivered in wheat starch
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
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: 2 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Polysaccharide-Based Injection Matrix for Serial Crystallography.
Authors: Nam, K.H.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)16,3293
Polymers16,2581
Non-polymers712
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.360, 79.360, 38.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 34.25 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→80 Å / Num. obs: 8796 / % possible obs: 100 % / Redundancy: 124.5 % / CC1/2: 0.9637 / CC star: 0.9916 / R split: 1.675E-6 / Net I/σ(I): 4.06
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.58 % / Num. unique obs: 840 / CC1/2: 0.6351 / CC star: 0.8924 / R split: 6.566E-6 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: commercial syringe / Flow rate: 0.2 µL/min / Injector diameter: 168 µm / Injector temperature: 298.15 K

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IG6

6ig6


Resolution: 2→56.116 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.83
RfactorNum. reflection% reflection
Rfree0.2333 878 10.01 %
Rwork0.1841 --
obs0.189 8768 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.09 Å2 / Biso mean: 38.5716 Å2 / Biso min: 20.92 Å2
Refinement stepCycle: final / Resolution: 2→56.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 50 1053
Biso mean--47.5 41.49 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0002-2.12550.30931420.26241276
2.1255-2.28960.29861420.23231283
2.2896-2.520.29021450.21911301
2.52-2.88470.26271440.21571292
2.8847-3.63430.25231470.18121329
3.6343-56.1160.18311580.15221409

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