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

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Basic information

Entry
Database: PDB / ID: 7ave
TitlePerdeuterated refolded hen egg-white lysozyme at 100 K
ComponentsLysozyme C
KeywordsHYDROLASE / Perdeuterated / refolded / lysozyme
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
ACETATE ION / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsRamos, J. / Laux, V. / Haertlein, M. / Erba Boeri, E. / Forsyth, V.T. / Larsen, S. / Mossou, E. / 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 1.2Jan 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
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)15,00211
Polymers14,3881
Non-polymers61410
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, MW = 15060 Da
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint10 kcal/mol
Surface area6740 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
Symmetry operation#1: x,y,z

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14388.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.7 Å3/Da / Density % sol: 27.56 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.5
Details: 0.15 M sodium nitrate, 0.05 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.98→32.01 Å / Num. obs: 52966 / % possible obs: 97.44 % / Redundancy: 5.3 % / Biso Wilson estimate: 7.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0424 / Rpim(I) all: 0.047 / Rrim(I) all: 0.053 / Net I/σ(I): 18.09
Reflection shellResolution: 0.98→1.015 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.21 / Num. unique obs: 5018 / CC1/2: 0.935 / Rpim(I) all: 0.136 / Rrim(I) all: 0.306 / % possible all: 92.67

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Processing

Software
NameVersionClassification
PHENIXv1.15.2refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YEO

4yeo


Resolution: 0.98→32.01 Å / SU ML: 0.0498 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 9.3646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1145 2510 4.74 %
Rwork0.1049 50453 -
obs0.1052 52964 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.96 Å2
Refinement stepCycle: LAST / Resolution: 0.98→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 40 136 1181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831367
X-RAY DIFFRACTIONf_angle_d1.4231874
X-RAY DIFFRACTIONf_chiral_restr0.0959183
X-RAY DIFFRACTIONf_plane_restr0.0143269
X-RAY DIFFRACTIONf_dihedral_angle_d13.4576805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-10.14071370.13632636X-RAY DIFFRACTION91.73
1-1.020.13721110.12512719X-RAY DIFFRACTION94.05
1.02-1.040.12361380.11352776X-RAY DIFFRACTION95.98
1.04-1.070.11241260.10212777X-RAY DIFFRACTION96.29
1.07-1.090.11321340.09412775X-RAY DIFFRACTION96.84
1.09-1.120.11451370.08832787X-RAY DIFFRACTION96.79
1.12-1.150.09581350.08642811X-RAY DIFFRACTION97
1.15-1.190.0981410.08372804X-RAY DIFFRACTION97.58
1.19-1.230.0981400.08352794X-RAY DIFFRACTION97.54
1.23-1.280.08911420.08272810X-RAY DIFFRACTION97.81
1.28-1.340.09621420.08552850X-RAY DIFFRACTION98.07
1.34-1.410.09971490.08432786X-RAY DIFFRACTION98.36
1.41-1.50.09931360.08752837X-RAY DIFFRACTION98.67
1.5-1.620.10261460.08572859X-RAY DIFFRACTION99.04
1.62-1.780.09791470.09562850X-RAY DIFFRACTION99.04
1.78-2.040.09351490.10142858X-RAY DIFFRACTION99.47
2.04-2.570.12051500.11382857X-RAY DIFFRACTION99.8
2.57-32.010.14511500.13362867X-RAY DIFFRACTION99.87

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