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- PDB-6qqd: Cryogenic temperature structure of Hen Egg White Lysozyme recorde... -

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Basic information

Entry
Database: PDB / ID: 6qqd
TitleCryogenic temperature structure of Hen Egg White Lysozyme recorded after an accumulated dose of 10 MGy
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: 1.92 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 23, 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)14,5447
Polymers14,3311
Non-polymers2136
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-57 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.960, 77.960, 37.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-384-

HOH

31A-405-

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 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.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 6-9% NaCl, 0.1M Na Acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.92→33.71 Å / Num. obs: 8490 / % possible obs: 91.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.699 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.34
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.88 / Num. unique obs: 640 / CC1/2: 0.706 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.92→33.71 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.628 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21594 431 5.1 %RANDOM
Rwork0.15247 ---
obs0.15577 8059 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.92→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 6 105 1109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121151
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181018
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6391591
X-RAY DIFFRACTIONr_angle_other_deg1.3761.5922372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6965.15167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69420.41772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05415192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7371514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02283
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_it41.2713.668568
X-RAY DIFFRACTIONr_mcbond_other35.6333.643568
X-RAY DIFFRACTIONr_mcangle_it37.6015.497721
X-RAY DIFFRACTIONr_mcangle_other41.7655.544722
X-RAY DIFFRACTIONr_scbond_it75.3394.546582
X-RAY DIFFRACTIONr_scbond_other72.1994.523582
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other59.6846.3852
X-RAY DIFFRACTIONr_long_range_B_refined53.70444.1641415
X-RAY DIFFRACTIONr_long_range_B_other54.11743.711390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 31 -
Rwork0.258 606 -
obs--95.79 %

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