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- PDB-6h79: SSX structure of Lysozyme in flow - metal-kapton microfluidic device -

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Basic information

Entry
Database: PDB / ID: 6h79
TitleSSX structure of Lysozyme in flow - metal-kapton microfluidic device
ComponentsLysozyme C
KeywordsHYDROLASE
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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMonteiro, D.C.F. / Trebbin, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationExzellenzcluster 1074 Germany
German Federal Ministry for Education and Research05K16GU1 Germany
CitationJournal: J.Synchrotron Radiat. / Year: 2019
Title: A microfluidic flow-focusing device for low sample consumption serial synchrotron crystallography experiments in liquid flow.
Authors: Monteiro, D.C.F. / Vakili, M. / Harich, J. / Sztucki, M. / Meier, S.M. / Horrell, S. / Josts, I. / Trebbin, M.
History
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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
Revision 1.2Oct 16, 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5115
Polymers14,3311
Non-polymers1804
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-17 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 79.300, 37.700
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-315-

HOH

21A-323-

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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 36 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 275 K / Method: batch mode / pH: 3.5
Details: 3:1 v/v precipitant solution:protein solution precipitant: 50 mM NaAc pH 3.5, 1M NaCl, 35% ethylene glycol, 20% PEG3350 protein buffer: 50 mM NaAc (pH 3.5)

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→56.07 Å / Num. obs: 7013 / % possible obs: 100 % / Redundancy: 121.1 % / Biso Wilson estimate: 52.38 Å2 / CC1/2: 0.96 / R split: 0.1158 / Net I/σ(I): 5.57
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 87.6 % / Mean I/σ(I) obs: 1.36 / CC1/2: 0.32 / R split: 1.13 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MJJ

5mjj


Resolution: 2.1→56.07 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.127 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21572 400 5.4 %RANDOM
Rwork0.16559 ---
obs0.16832 7013 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.1→56.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 10 32 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131049
X-RAY DIFFRACTIONr_bond_other_d0.0010.018936
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.641420
X-RAY DIFFRACTIONr_angle_other_deg1.3571.5882156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9272065
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88415172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9571513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021217
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02258
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_it3.1685.066520
X-RAY DIFFRACTIONr_mcbond_other3.155.055518
X-RAY DIFFRACTIONr_mcangle_it4.0597.584648
X-RAY DIFFRACTIONr_mcangle_other4.0627.591649
X-RAY DIFFRACTIONr_scbond_it4.4225.562529
X-RAY DIFFRACTIONr_scbond_other4.4185.562530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4698.172771
X-RAY DIFFRACTIONr_long_range_B_refined8.08259.1981246
X-RAY DIFFRACTIONr_long_range_B_other8.07859.1831244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 21 -
Rwork0.318 515 -
obs--100 %

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