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- PDB-7llp: X-ray radiation damage series on Lysozyme at 277K, crystal struct... -

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Basic information

Entry
Database: PDB / ID: 7llp
TitleX-ray radiation damage series on Lysozyme at 277K, crystal structure, dataset 1
ComponentsLysozyme C
KeywordsHYDROLASE / radiation damage / conformational heterogeneity / antimicrobial enzyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 4, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
Water2,090116
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-326-

HOH

21A-332-

HOH

31A-374-

HOH

41A-416-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 0.1212 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.8231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1546 2160 5.07 %
Rwork0.1316 40437 -
obs0.1327 42597 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 1.13→34.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 116 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781285
X-RAY DIFFRACTIONf_angle_d0.99211761
X-RAY DIFFRACTIONf_chiral_restr0.0796176
X-RAY DIFFRACTIONf_plane_restr0.007247
X-RAY DIFFRACTIONf_dihedral_angle_d13.5056490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.32691240.30442538X-RAY DIFFRACTION95.79
1.16-1.190.27681360.26362641X-RAY DIFFRACTION99.11
1.19-1.220.26641290.23452684X-RAY DIFFRACTION99.82
1.22-1.250.24591580.21912640X-RAY DIFFRACTION99.75
1.25-1.290.20011430.17912676X-RAY DIFFRACTION99.93
1.29-1.340.19761370.1682679X-RAY DIFFRACTION99.96
1.34-1.390.16381390.13942671X-RAY DIFFRACTION99.89
1.39-1.460.16151520.12022677X-RAY DIFFRACTION99.89
1.46-1.530.14721510.10162675X-RAY DIFFRACTION99.82
1.53-1.630.11041490.10212697X-RAY DIFFRACTION99.89
1.63-1.760.12591410.10292712X-RAY DIFFRACTION99.96
1.76-1.930.13591360.10372718X-RAY DIFFRACTION100
1.93-2.210.12011570.10472744X-RAY DIFFRACTION99.97
2.21-2.790.14961510.11922758X-RAY DIFFRACTION99.97
2.79-34.550.1591570.13922927X-RAY DIFFRACTION99.87

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