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- PDB-7avg: Perdeuterated hen egg-white lysozyme at 100 K -

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Basic information

Entry
Database: PDB / ID: 7avg
TitlePerdeuterated hen egg-white lysozyme at 100 K
ComponentsLysozyme
KeywordsHYDROLASE / perdeuterated / lysozyme / hewl
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
ACETATE ION / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsRamos, J. / Laux, V. / Haertlein, M. / Erba Boeri, E. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E.
CitationJournal: Iucrj / Year: 2021
Title: Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme.
Authors: Ramos, J. / Laux, V. / Haertlein, M. / Boeri Erba, E. / McAuley, K.E. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 14, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,94511
Polymers14,3311
Non-polymers61410
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, 15006 Da
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint10 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.670, 30.970, 33.740
Angle α, β, γ (deg.)89.439, 72.818, 67.503
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Komagataella pastoris (fungus) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.7 Å3/Da / Density % sol: 27.84 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 4.5 / Details: sodium nitrate, sodium acetate pD 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7999 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 1→32.01 Å / Num. obs: 49991 / % possible obs: 97.71 % / Redundancy: 6.7 % / Biso Wilson estimate: 8.81 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.0803 / Rpim(I) all: 0.0344 / Rrim(I) all: 0.0876 / Net I/σ(I): 15.07
Reflection shellResolution: 1→1.036 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 6.92 / Num. unique obs: 4880 / CC1/2: 0.979 / Rpim(I) all: 0.109 / Rrim(I) all: 0.284 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4yeo

4yeo


Resolution: 1→32.01 Å / SU ML: 0.0642 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 11.4961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1341 2400 4.8 %
Rwork0.1205 47582 -
obs0.121 49982 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.84 Å2
Refinement stepCycle: LAST / Resolution: 1→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 40 135 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271376
X-RAY DIFFRACTIONf_angle_d1.61631889
X-RAY DIFFRACTIONf_chiral_restr0.1038186
X-RAY DIFFRACTIONf_plane_restr0.0146271
X-RAY DIFFRACTIONf_dihedral_angle_d13.4583806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.13781230.12182747X-RAY DIFFRACTION95.13
1.02-1.040.12911320.11372739X-RAY DIFFRACTION95.83
1.04-1.070.14191340.10532781X-RAY DIFFRACTION96.24
1.07-1.090.13191360.09992739X-RAY DIFFRACTION96.44
1.09-1.120.13291350.09662767X-RAY DIFFRACTION96.8
1.12-1.160.12051370.09462786X-RAY DIFFRACTION97.01
1.16-1.190.10131440.09092786X-RAY DIFFRACTION97.18
1.19-1.240.11291470.09082805X-RAY DIFFRACTION97.72
1.24-1.290.11211430.08672808X-RAY DIFFRACTION97.91
1.29-1.340.10951450.0942823X-RAY DIFFRACTION98.34
1.34-1.420.11551470.09472788X-RAY DIFFRACTION98.26
1.42-1.50.1261380.10122820X-RAY DIFFRACTION98.63
1.5-1.620.12761460.10122844X-RAY DIFFRACTION98.84
1.62-1.780.13281490.11482834X-RAY DIFFRACTION99.1
1.78-2.040.12141480.12162843X-RAY DIFFRACTION99.4
2.04-2.570.13771490.12852838X-RAY DIFFRACTION99.37
2.57-32.010.15571470.15462834X-RAY DIFFRACTION99

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