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- PDB-7ln9: X-ray radiation damage series on Lysozyme at 277K, multi-conforme... -

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Basic information

Entry
Database: PDB / ID: 7ln9
TitleX-ray radiation damage series on Lysozyme at 277K, multi-conformer model, dataset 1
ComponentsLysozyme C
KeywordsHYDROLASE / radiation damage / conformational heterogeneity / antimicrobial enzyme
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: 1.13 Å
AuthorsYabukarski, F. / Doukov, T. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.
Authors: Yabukarski, F. / Doukov, T. / Mokhtari, D.A. / Du, S. / Herschlag, D.
History
DepositionFeb 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3903
Polymers14,3311
Non-polymers582
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.258, 77.258, 37.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-371-

HOH

31A-412-

HOH

41A-413-

HOH

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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) / 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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Lysozyme was dissolved in 0.1 M Sodium Acetate pH 4.6 at 100 mg/ml and 5 microliters of this protein solution was mixed with 5 microliters of 0.1 M Sodium Acetate and 0.6 M Sodium Chloride ...Details: Lysozyme was dissolved in 0.1 M Sodium Acetate pH 4.6 at 100 mg/ml and 5 microliters of this protein solution was mixed with 5 microliters of 0.1 M Sodium Acetate and 0.6 M Sodium Chloride solution pH 4.6. The 10 microliters drop was equilibrated against 0.7 milliliters of 2.2 M Ammonium sulfate well solution.

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.13→38.63 Å / Num. obs: 42780 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 14.15 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Net I/σ(I): 12.4
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 8.4 % / Rmerge(I) obs: 2.72 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2047 / Rpim(I) all: 0.989 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.13→34.55 Å / SU ML: 0.1189 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.156 2160 5.07 %
Rwork0.1359 40437 -
obs0.1369 42597 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.13→34.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 2 113 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632976
X-RAY DIFFRACTIONf_angle_d0.83674014
X-RAY DIFFRACTIONf_chiral_restr0.0697424
X-RAY DIFFRACTIONf_plane_restr0.0046523
X-RAY DIFFRACTIONf_dihedral_angle_d13.0971067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.31961240.31012538X-RAY DIFFRACTION95.79
1.16-1.190.27021360.27442641X-RAY DIFFRACTION99.11
1.19-1.220.29761290.24772684X-RAY DIFFRACTION99.82
1.22-1.250.25631580.23182640X-RAY DIFFRACTION99.75
1.25-1.290.2011430.19812676X-RAY DIFFRACTION99.93
1.29-1.340.21191370.18592679X-RAY DIFFRACTION99.96
1.34-1.390.1661390.16132671X-RAY DIFFRACTION99.89
1.39-1.460.15951520.1382677X-RAY DIFFRACTION99.89
1.46-1.530.15681510.12152675X-RAY DIFFRACTION99.82
1.53-1.630.14361490.1212697X-RAY DIFFRACTION99.89
1.63-1.760.14031410.11562712X-RAY DIFFRACTION99.96
1.76-1.930.13341360.11222718X-RAY DIFFRACTION100
1.93-2.210.12621570.10962744X-RAY DIFFRACTION99.97
2.21-2.790.14421510.12082758X-RAY DIFFRACTION99.97
2.79-34.550.15231570.13222927X-RAY DIFFRACTION99.87

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