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- PDB-6gf0: Lysozyme structure determined from SFX data using a Sheet-on-Shee... -

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Basic information

Entry
Database: PDB / ID: 6gf0
TitleLysozyme structure determined from SFX data using a Sheet-on-Sheet chipless chip
ComponentsLysozyme C
KeywordsHYDROLASE / SERIAL CRYSTALLOGRAPHY / FREE-ELECTRON LASER / CHIP CRYSTALLOGRAPHY
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsDoak, R.B. / Gorel, A. / Foucar, L. / Gruenbein, M.L. / Hilpert, M. / Kloos, M. / Nass Kovacs, G. / Roome, C. / Shoeman, R.L. / Stricker, M. ...Doak, R.B. / Gorel, A. / Foucar, L. / Gruenbein, M.L. / Hilpert, M. / Kloos, M. / Nass Kovacs, G. / Roome, C. / Shoeman, R.L. / Stricker, M. / Tono, K. / You, D. / Ueda, K. / Sherrel, D. / Owen, R. / Barends, T.R.M. / Schlichting, I.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystallography on a chip - without the chip: sheet-on-sheet sandwich.
Authors: Doak, R.B. / Nass Kovacs, G. / Gorel, A. / Foucar, L. / Barends, T.R.M. / Grunbein, M.L. / Hilpert, M. / Kloos, M. / Roome, C.M. / Shoeman, R.L. / Stricker, M. / Tono, K. / You, D. / Ueda, K. ...Authors: Doak, R.B. / Nass Kovacs, G. / Gorel, A. / Foucar, L. / Barends, T.R.M. / Grunbein, M.L. / Hilpert, M. / Kloos, M. / Roome, C.M. / Shoeman, R.L. / Stricker, M. / Tono, K. / You, D. / Ueda, K. / Sherrell, D.A. / Owen, R.L. / Schlichting, I.
History
DepositionApr 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Structure summary / Category: diffrn / entity
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight
Revision 1.2Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.100, 79.100, 39.200
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-213-

HOH

21A-243-

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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 20 % NaCl, 6 % PEG 6000, 0.1 M sodium acetate pH 3.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.07→40 Å / Num. obs: 7417 / % possible obs: 100 % / Redundancy: 283 % / CC1/2: 0.986 / R split: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 42 % / Mean I/σ(I) obs: 2.8 / CC1/2: 0.773 / R split: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4n5r

4n5r


Resolution: 2.07→39.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.616 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23483 385 4.9 %RANDOM
Rwork0.19862 ---
obs0.20034 7417 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.191 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: 1 / Resolution: 2.07→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 43 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191016
X-RAY DIFFRACTIONr_bond_other_d0.0010.02929
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.8971376
X-RAY DIFFRACTIONr_angle_other_deg0.79132115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0882350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61515164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2551511
X-RAY DIFFRACTIONr_chiral_restr0.0530.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
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_it0.8513.005511
X-RAY DIFFRACTIONr_mcbond_other0.853.003510
X-RAY DIFFRACTIONr_mcangle_it1.4584.501637
X-RAY DIFFRACTIONr_mcangle_other1.4574.504638
X-RAY DIFFRACTIONr_scbond_it1.0893.188505
X-RAY DIFFRACTIONr_scbond_other1.0883.193506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8984.716740
X-RAY DIFFRACTIONr_long_range_B_refined3.21724.2841199
X-RAY DIFFRACTIONr_long_range_B_other3.21524.2831195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.074→2.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 12 -
Rwork0.45 410 -
obs--73.91 %

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