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- PDB-5myy: Hen Egg-White Lysozyme (HEWL) cocrystallized in the presence of C... -

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Basic information

Entry
Database: PDB / ID: 5myy
TitleHen Egg-White Lysozyme (HEWL) cocrystallized in the presence of Cadmium sulphate
ComponentsLysozyme C
KeywordsHYDROLASE / SAD phasing / Cadmium phasing / 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
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 / SAD / Resolution: 1.1 Å
AuthorsPanneerselvam, S. / Burkhardt, A. / Meents, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Rapid cadmium SAD phasing at the standard wavelength (1 angstrom ).
Authors: Panneerselvam, S. / Kumpula, E.P. / Kursula, I. / Burkhardt, A. / Meents, A.
History
DepositionJan 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Oct 16, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_special_symmetry ...atom_site / pdbx_struct_special_symmetry / pdbx_validate_symm_contact / reflns_shell
Item: _atom_site.occupancy

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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)15,89523
Polymers14,3311
Non-polymers1,56422
Water2,126118
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-168 kcal/mol
Surface area6370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.740, 78.740, 37.010
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-352-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 140 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate pH 4.8 10-12% NaCl 20-25% Ethylene Glycol 60 mg/ ml HEWL in 0.1 M Sodium acetate pH 4.8

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.1→39.37 Å / Num. obs: 47744 / % possible obs: 100 % / Redundancy: 28 % / Net I/σ(I): 55

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→55.68 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.541 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14305 953 2 %RANDOM
Rwork0.12987 ---
obs0.13013 46766 99.95 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.6 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0 Å2
2--0.27 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.1→55.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 25 118 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191064
X-RAY DIFFRACTIONr_bond_other_d0.0020.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9021446
X-RAY DIFFRACTIONr_angle_other_deg1.12132156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22323.14854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88415172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.431512
X-RAY DIFFRACTIONr_chiral_restr0.1320.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021238
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02246
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_it1.0181.281532
X-RAY DIFFRACTIONr_mcbond_other1.0141.277531
X-RAY DIFFRACTIONr_mcangle_it1.4411.929669
X-RAY DIFFRACTIONr_mcangle_other1.4461.933670
X-RAY DIFFRACTIONr_scbond_it1.7741.539532
X-RAY DIFFRACTIONr_scbond_other1.7731.539532
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8732.224777
X-RAY DIFFRACTIONr_long_range_B_refined3.79416.3331319
X-RAY DIFFRACTIONr_long_range_B_other3.48816.1111304
X-RAY DIFFRACTIONr_rigid_bond_restr2.88631996
X-RAY DIFFRACTIONr_sphericity_free21.6085102
X-RAY DIFFRACTIONr_sphericity_bonded7.99552007
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.128 67 -
Rwork0.102 3393 -
obs--99.34 %

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