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- PDB-6qqf: Room temperature structure of Hen Egg White Lysozyme recorded aft... -

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Basic information

Entry
Database: PDB / ID: 6qqf
TitleRoom temperature structure of Hen Egg White Lysozyme recorded after an accumulated dose of 100 kGy
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / disulphide bonds / radiation damage
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 / Resolution: 1.95 Å
AuthorsGotthard, G. / Aumonier, S. / Royant, A.
CitationJournal: Iucrj / Year: 2019
Title: Specific radiation damage is a lesser concern at room temperature.
Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A.
History
DepositionFeb 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4023
Polymers14,3311
Non-polymers712
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.010, 79.010, 38.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 6-9% NaCl, 0.1M Na Acetate pH4.8

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2018
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.95→39.51 Å / Num. obs: 9218 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.741 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.45
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.73 / Num. unique obs: 665 / CC1/2: 0.708 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 1.95→39.51 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.849 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22987 487 5.3 %RANDOM
Rwork0.15238 ---
obs0.15675 8732 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.95→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 2 71 1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121144
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181007
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.6391572
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5882341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0665158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26921.15969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66815182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9221512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it18.0452.792575
X-RAY DIFFRACTIONr_mcbond_other17.9822.781574
X-RAY DIFFRACTIONr_mcangle_it18.5284.185725
X-RAY DIFFRACTIONr_mcangle_other18.574.19726
X-RAY DIFFRACTIONr_scbond_it3.704569
X-RAY DIFFRACTIONr_scbond_other3.701569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other84.9975.046836
X-RAY DIFFRACTIONr_long_range_B_refined83.18233.4471319
X-RAY DIFFRACTIONr_long_range_B_other83.46133.2881310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 31 -
Rwork0.201 635 -
obs--99.85 %

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