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- PDB-7l84: Hen Egg White Lysozyme by Native S-SAD at Room Temperature -

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Basic information

Entry
Database: PDB / ID: 7l84
TitleHen Egg White Lysozyme by Native S-SAD at Room Temperature
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 / SAD / Resolution: 1.7 Å
AuthorsGreisman, J.B. / Dalton, K.M. / Hekstra, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
Searle Scholars ProgramSSP-2018-3240 United States
The George W. Merck Fund in the New York Community Trust338034 United States
National Science Foundation (NSF, United States)DGE1745303 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Native SAD phasing at room temperature.
Authors: Greisman, J.B. / Dalton, K.M. / Sheehan, C.J. / Klureza, M.A. / Kurinov, I. / Hekstra, D.R.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6550 Å2
Unit cell
Length a, b, c (Å)79.344, 79.344, 37.810
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-239-

HOH

21A-292-

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM citrate buffer (pH 5.2 - 5.8), 20-25% PEG 4000, 20-25% glycerol
PH range: 5.2 - 5.8

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Data collection

DiffractionMean temperature: 295 K / Ambient temp details: Ambient temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.892 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.892 Å / Relative weight: 1
ReflectionResolution: 1.7→56.1 Å / Num. obs: 22855 / % possible obs: 90.74 % / Redundancy: 35.7 % / Biso Wilson estimate: 17.21 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1022 / Rpim(I) all: 0.01461 / Rrim(I) all: 0.1033 / Net I/σ(I): 35.63
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 767 / CC1/2: 0.968 / CC star: 0.992 / Rpim(I) all: 0.08357 / Rrim(I) all: 0.2078 / % possible all: 30.45

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Processing

Software
NameVersionClassification
DIALS3.1.4data reduction
Aimless0.7.4data scaling
AutoSol1.18.2_3874phasing
PHENIX1.18.2_3874model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→56.1 Å / SU ML: 0.1652 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.0408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1621 1121 4.9 %
Rwork0.1396 21735 -
obs0.1409 22855 90.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→56.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 97 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851143
X-RAY DIFFRACTIONf_angle_d0.91011558
X-RAY DIFFRACTIONf_chiral_restr0.0549157
X-RAY DIFFRACTIONf_plane_restr0.006212
X-RAY DIFFRACTIONf_dihedral_angle_d12.6524430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.780.2262590.15761090X-RAY DIFFRACTION36.66
1.78-1.880.18771360.13332731X-RAY DIFFRACTION90.58
1.88-1.990.13191330.1283024X-RAY DIFFRACTION99.56
1.99-2.150.15771480.10622962X-RAY DIFFRACTION99.46
2.15-2.360.14021600.13572988X-RAY DIFFRACTION99.71
2.36-2.710.15281620.13132970X-RAY DIFFRACTION99.94
2.71-3.410.16341600.14122984X-RAY DIFFRACTION99.87
3.41-56.10.1751630.15912986X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 38.939401791 Å / Origin y: 19.1055927678 Å / Origin z: 9.2710416792 Å
111213212223313233
T0.0645705332377 Å22.47641910749E-5 Å20.00164815979428 Å2-0.0801332437814 Å2-0.0201346579165 Å2--0.0804149023324 Å2
L2.5280687995 °20.831818792036 °2-0.380353504149 °2-2.49911761502 °2-0.245999324086 °2--2.18094458614 °2
S-0.0119629544713 Å °0.0176187672436 Å °0.0451270044401 Å °-0.0291153676756 Å °0.0282362184297 Å °0.113328295349 Å °-0.0609384794063 Å °-0.0366574228773 Å °-0.00723340701229 Å °
Refinement TLS groupSelection details: all

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