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- PDB-7nkf: Hen egg white lysozyme (HEWL) Grown inside (Not centrifuged) HARE... -

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Basic information

Entry
Database: PDB / ID: 7nkf
TitleHen egg white lysozyme (HEWL) Grown inside (Not centrifuged) HARE serial crystallography chip.
ComponentsLysozyme
KeywordsHYDROLASE / serial crystallography / lysozyme / vapour diffusion / silicon chip
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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNorton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip.
Authors: Norton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Kwok, A.O. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
History
DepositionFeb 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,3542
Polymers14,3311
Non-polymers231
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.800, 78.800, 38.700
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-356-

HOH

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Components

#1: Protein Lysozyme


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 33% PEG 4000, 0.5 M NaCl, 50 mM sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→55.72 Å / Num. obs: 13921 / % possible obs: 100 % / Redundancy: 174 % / Biso Wilson estimate: 19.79 Å2 / CC1/2: 0.9525 / Net I/σ(I): 6.8
Reflection shellResolution: 1.7→1.83 Å / Num. unique obs: 1358 / CC1/2: 0.8962
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPX

1dpx


Resolution: 1.7→55.72 Å / SU ML: 0.1731 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2118 697 5.01 %
Rwork0.175 13224 -
obs0.1766 13921 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 1 74 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01251044
X-RAY DIFFRACTIONf_angle_d1.25431412
X-RAY DIFFRACTIONf_chiral_restr0.0826147
X-RAY DIFFRACTIONf_plane_restr0.0078185
X-RAY DIFFRACTIONf_dihedral_angle_d20.2648379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.22551360.18362588X-RAY DIFFRACTION100
1.83-2.020.22991360.16982575X-RAY DIFFRACTION100
2.02-2.310.21261380.16192623X-RAY DIFFRACTION100
2.31-2.910.23031390.18662640X-RAY DIFFRACTION100
2.91-55.720.19651480.17362798X-RAY DIFFRACTION100

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