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- PDB-5ebh: Crystal Structure HEW Lysozyme processed with the CrystalDirect a... -

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Basic information

Entry
Database: PDB / ID: 5ebh
TitleCrystal Structure HEW Lysozyme processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsLysozyme C
KeywordsHYDROLASE / Glycosylase
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZander, U. / Hoffmann, G. / Cornaciu, I. / Marquez, J.A.
Funding support France, 1items
OrganizationGrant numberCountry
European Commission283570 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Automated harvesting and processing of protein crystals through laser photoablation.
Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jan 10, 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
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.801, 78.801, 37.267
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-212-

HOH

21A-296-

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.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Crystallization experiments were carried out at the High Throughput Crystallization Laboratory of the EMBL Grenoble Outstation (https://embl.fr/htxlab) using the sitting-drop vapour ...Details: Crystallization experiments were carried out at the High Throughput Crystallization Laboratory of the EMBL Grenoble Outstation (https://embl.fr/htxlab) using the sitting-drop vapour diffusion method and CrystalDirect plates . Crystallization experiments were set up with 100 nl of sample and 100 nl of crystallization solution on the inner surface of the films within a CrystalDirect plate with a Cartesian PixSys robot (Cartesian Technologies). The crystallization solution was 0.1 M sodium acetate, pH=4.6 and 1.25 M sodium chloride.
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.2→19.7 Å / Num. obs: 37274 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 1.2→1.22 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b0d

4b0d


Resolution: 1.2→19.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.494 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20102 1896 5.1 %RANDOM
Rwork0.17308 ---
obs0.17452 35325 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 215 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191036
X-RAY DIFFRACTIONr_bond_other_d0.0020.02931
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9051412
X-RAY DIFFRACTIONr_angle_other_deg2.1832131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.9125136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36424.1346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67515163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.846158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021241
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02265
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_it0.661.228537
X-RAY DIFFRACTIONr_mcbond_other0.5191.227536
X-RAY DIFFRACTIONr_mcangle_it0.7181.85673
X-RAY DIFFRACTIONr_mcangle_other0.7661.851674
X-RAY DIFFRACTIONr_scbond_it0.6441.33499
X-RAY DIFFRACTIONr_scbond_other0.5681.33499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7121.961738
X-RAY DIFFRACTIONr_long_range_B_refined2.06211.8871422
X-RAY DIFFRACTIONr_long_range_B_other1.36110.6111294
X-RAY DIFFRACTIONr_rigid_bond_restr4.03531966
X-RAY DIFFRACTIONr_sphericity_free17.92565
X-RAY DIFFRACTIONr_sphericity_bonded4.06852090
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 149 -
Rwork0.238 2537 -
obs--99.96 %

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