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- PDB-8reh: Lysozyme measured via serial crystallography from a kapton HARE-c... -

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Basic information

Entry
Database: PDB / ID: 8reh
TitleLysozyme measured via serial crystallography from a kapton HARE-chip (125 micron)
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / enzyme / muramidase
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
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-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Economic Affairs and Energy01KI2114 Germany
CitationJournal: To Be Published
Title: Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Blatter, G. / Lu, G. / Bernhard, S. / Osbild, M. / Schulz, E.C.
History
DepositionDec 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4725
Polymers14,3311
Non-polymers1404
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-14 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 79.000, 38.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-338-

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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 293.15 K / Method: batch mode / Details: 100mg/ml NaCl

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.38→55.86 Å / Num. obs: 15648 / % possible obs: 95.16 % / Redundancy: 657.8 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.986 / CC star: 0.996 / R split: 0.0883 / Net I/σ(I): 12.02
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 347.7 % / Mean I/σ(I) obs: 8.84 / Num. unique obs: 1349 / CC1/2: 0.975 / CC star: 0.994 / R split: 0.1102 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: Hare-Chip , Caption

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.86 Å / SU ML: 0.1894 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.1021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1753 693 5.04 %
Rwork0.1681 13061 -
obs0.1685 13754 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 64 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681086
X-RAY DIFFRACTIONf_angle_d0.90841478
X-RAY DIFFRACTIONf_chiral_restr0.0596155
X-RAY DIFFRACTIONf_plane_restr0.0104195
X-RAY DIFFRACTIONf_dihedral_angle_d5.8391162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.25661340.21022564X-RAY DIFFRACTION99.93
1.83-2.020.16331440.14552545X-RAY DIFFRACTION100
2.02-2.310.19441350.16612576X-RAY DIFFRACTION99.96
2.31-2.910.19331260.17262629X-RAY DIFFRACTION100
2.91-55.860.15231540.16482747X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.6259802532 Å / Origin y: 0.583545487698 Å / Origin z: -0.335677223413 Å
111213212223313233
T0.0891295517619 Å2-0.00858169234255 Å2-0.0127868868648 Å2-0.0772897844931 Å20.00337016975154 Å2--0.0867395567973 Å2
L1.90726456844 °2-0.809280587894 °2-0.115200313938 °2-2.03515732002 °20.246026474532 °2--1.4850736424 °2
S0.0214375212498 Å °0.0363194358738 Å °0.0953916775787 Å °-0.0200106897002 Å °-0.0252965243272 Å °-0.0497493843547 Å °-0.0352192032541 Å °0.0429154488676 Å °-0.00449166072496 Å °
Refinement TLS groupSelection details: all

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