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- PDB-4hv2: Laser-induced microfragmentation of lysozyme crystals allows X-ra... -

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Basic information

Entry
Database: PDB / ID: 4hv2
TitleLaser-induced microfragmentation of lysozyme crystals allows X-ray nanodiffraction characterization of individual domains (lb5)
ComponentsLysozyme C
KeywordsHYDROLASE / Protein nanocrystallography / protein crystallization / laser-microdissection / crystal domains
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å
AuthorsPechkova, E. / Belmonte, L. / Riekel, C. / Popov, D. / Koenig, C. / Nicolini, C.
CitationJournal: To be Published
Title: Laser-induced microfragmentation of lysozyme crystals allows X-ray nanodiffraction characterization of individual domains
Authors: Pechkova, E. / Belmonte, L. / Riekel, C. / Popov, D. / Koenig, C. / Nicolini, C.
History
DepositionNov 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.703, 79.703, 37.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: LB-nanofilms were generated by the Langmuir Blodgett (LB) technique and its variation, a modified Langmuir Schaeffer technique (LS). 40 mg/ml, 50 mM, sodium acetate pH 4.5, 0.9 NaCl 1:1 in ...Details: LB-nanofilms were generated by the Langmuir Blodgett (LB) technique and its variation, a modified Langmuir Schaeffer technique (LS). 40 mg/ml, 50 mM, sodium acetate pH 4.5, 0.9 NaCl 1:1 in 50 mM sodium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.525→56.359 Å / Num. all: 4465 / Num. obs: 3371 / % possible obs: 78.9 % / Redundancy: 4.6 % / Rsym value: 0.432 / Net I/σ(I): 3.1
Reflection shell

Rmerge(I) obs: 0.026 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.525-1.612.70.3464817442.61265.1
1.61-1.714.70.21009721634.14985.1
1.71-1.824.80.3961420213.01984.6
1.82-1.974.80.5900218611.63382.8
1.97-2.164.90.9827916960.87482.2
2.16-2.414.91.4752615230.51680.7
2.41-2.7852664213180.35878.8
2.78-3.415.13.5571611160.19877
3.41-4.825.15.743618520.11474.7
4.82-39.8524.86.123744910.10471.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.57 Å39.85 Å
Translation2.57 Å39.85 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.501→56.359 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.772 / WRfactor Rfree: 0.3097 / WRfactor Rwork: 0.1872 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8093 / SU B: 11.308 / SU ML: 0.254 / SU Rfree: 0.5089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3186 154 4.6 %RANDOM
Rwork0.1999 ---
obs0.2053 3359 75.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.07 Å2 / Biso mean: 10.3664 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.501→56.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 47 1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211025
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9031389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6252350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53415166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.011511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02794
X-RAY DIFFRACTIONr_mcbond_it0.5531.5635
X-RAY DIFFRACTIONr_mcangle_it1.13421008
X-RAY DIFFRACTIONr_scbond_it2.0033390
X-RAY DIFFRACTIONr_scangle_it3.2624.5381
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 15 -
Rwork0.228 234 -
all-249 -
obs--79.3 %

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