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

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Basic information

Entry
Database: PDB / ID: 7lpl
TitleX-ray radiation damage series on Lysozyme at 277K, multi-conformer model, dataset 3 (merged)
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: 1.14 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 12, 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 1.3Oct 16, 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
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 77.260, 37.260
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-322-

HOH

21A-367-

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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 36.59 %
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: 1.14→38.6 Å / Num. obs: 41673 / % possible obs: 100 % / Redundancy: 59.2 % / Biso Wilson estimate: 15.57 Å2 / Rmerge(I) obs: 0.411 / Rpim(I) all: 0.054 / Net I/σ(I): 19.3
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 51.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2032 / Rpim(I) all: 7.853 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LLP

7llp


Resolution: 1.14→34.55 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1581 2105 5.06 %
Rwork0.1366 39485 -
obs0.1377 41590 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.33 Å2
Refinement stepCycle: LAST / Resolution: 1.14→34.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 2 113 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642976
X-RAY DIFFRACTIONf_angle_d0.84564014
X-RAY DIFFRACTIONf_chiral_restr0.0699424
X-RAY DIFFRACTIONf_plane_restr0.0046523
X-RAY DIFFRACTIONf_dihedral_angle_d13.14321067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.31291160.31372562X-RAY DIFFRACTION97.81
1.17-1.20.30541380.27342565X-RAY DIFFRACTION99.96
1.2-1.230.26881320.23972612X-RAY DIFFRACTION99.96
1.23-1.260.24871500.23312576X-RAY DIFFRACTION99.82
1.26-1.30.21081350.19672594X-RAY DIFFRACTION99.96
1.3-1.350.21240.17332630X-RAY DIFFRACTION100
1.35-1.410.17851530.15252601X-RAY DIFFRACTION99.89
1.41-1.470.15011370.13272607X-RAY DIFFRACTION99.93
1.47-1.550.16461540.1212598X-RAY DIFFRACTION99.93
1.55-1.640.13651400.11732630X-RAY DIFFRACTION100
1.64-1.770.14681350.11862639X-RAY DIFFRACTION100
1.77-1.950.12811390.11482668X-RAY DIFFRACTION100
1.95-2.230.13261510.11342643X-RAY DIFFRACTION100
2.23-2.810.14631450.12622712X-RAY DIFFRACTION99.97
2.81-34.550.15961560.1362848X-RAY DIFFRACTION100

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