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- PDB-6rxi: In-flow serial synchrotron crystallography using a 3D-printed mic... -

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Basic information

Entry
Database: PDB / ID: 6rxi
TitleIn-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-MiXD): Lysozyme
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
DI(HYDROXYETHYL)ETHER / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMonteiro, D.C.F. / von Stetten, D. / Pearson, A.R. / Trebbin, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEXC 1074 - projectID 194651731 Germany
German Federal Ministry for Education and Research05K16GUI Germany
CitationJournal: Iucrj / Year: 2020
Title: 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow.
Authors: Monteiro, D.C.F. / von Stetten, D. / Stohrer, C. / Sans, M. / Pearson, A.R. / Santoni, G. / van der Linden, P. / Trebbin, M.
History
DepositionJun 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,6025
Polymers14,3311
Non-polymers2714
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-15 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.700, 79.700, 38.550
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-324-

HOH

21A-349-

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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.14 Å3/Da / Density % sol: 42.65 % / Description: cuboid microcrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 3
Details: 30 mg/mL lysozyme in 100 mM NaAc (pH3.0) rapidly mixed in a 1:1 ratio with precipitant (100 mM NaAc pH 3.0, 20% NaCl, 6% PEG 6000)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2→56.36 Å / Num. obs: 8876 / % possible obs: 100 % / Redundancy: 625 % / Biso Wilson estimate: 31.3 Å2 / R split: 0.06 / Net I/σ(I): 6.21
Reflection shellResolution: 2→2.08 Å / Redundancy: 448 % / Mean I/σ(I) obs: 1.83 / Num. unique obs: 869 / R split: 0.57 / % possible all: 100
Serial crystallography measurementCollection time total: 1 hours
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: crystallization buffer / Description: 3D-printed microfluidic device / Flow rate: 0.83 µL/min
Serial crystallography data reductionFrames indexed: 450000 / Frames total: 1000000

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
MOLREP11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H79

6h79


Resolution: 2→56.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.718 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20117 404 4.6 %RANDOM
Rwork0.15781 ---
obs0.15984 8437 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2→56.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 10 49 1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131069
X-RAY DIFFRACTIONr_bond_other_d0.0010.018964
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6391448
X-RAY DIFFRACTIONr_angle_other_deg1.3841.5922231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47720.15266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72615181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.451513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
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_it2.9723.625525
X-RAY DIFFRACTIONr_mcbond_other2.9523.616524
X-RAY DIFFRACTIONr_mcangle_it3.6435.411656
X-RAY DIFFRACTIONr_mcangle_other3.6635.419657
X-RAY DIFFRACTIONr_scbond_it4.1794.184544
X-RAY DIFFRACTIONr_scbond_other4.1754.189545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3736.072788
X-RAY DIFFRACTIONr_long_range_B_refined7.77141.4541230
X-RAY DIFFRACTIONr_long_range_B_other7.77441.4291226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 29 -
Rwork0.279 623 -
obs--99.85 %

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