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- PDB-3zek: Hen egg-white lysozyme structure determined at room temperature b... -

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Basic information

Entry
Database: PDB / ID: 3zek
TitleHen egg-white lysozyme structure determined at room temperature by in- situ diffraction in ChipX
ComponentsLYSOZYME C
KeywordsHYDROLASE / MICROFLUIDIC CHIP / IN-SITU DIFFRACTION
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: 1.43 Å
AuthorsPinker, F. / Lorber, B. / Sauter, C.
Citation
Journal: To be Published
Title: Chipx: A Novel Microfluidic Chip for Counter- Diffusion Crystallization of Biomolecules and in Situ Crystal Analysis at Room Temperature
Authors: Pinker, F. / Brun, M. / Morin, P. / Deman, A. / Chateaux, J. / Olieric, V. / Stirnimann, C. / Lorber, B. / Terrier, N. / Ferrigno, R. / Sauter, C.
#1: Journal: Lab Chip / Year: 2009
Title: Microfluidic Chips for the Crystallization of Biomacromolecules by Counter-Diffusion and on-Chip Crystal X-Ray Analysis.
Authors: Dhouib, K. / Khan Malek, C. / Pfleging, W. / Gauthier-Manuel, B. / Duffait, R. / Thuillier, G. / Ferrigno, R. / Jacquamet, L. / Ohana, J. / Ferrer, J. / Theobald-Dietrich, A. / Giege, R. / ...Authors: Dhouib, K. / Khan Malek, C. / Pfleging, W. / Gauthier-Manuel, B. / Duffait, R. / Thuillier, G. / Ferrigno, R. / Jacquamet, L. / Ohana, J. / Ferrer, J. / Theobald-Dietrich, A. / Giege, R. / Lorber, B. / Sauter, C.
History
DepositionDec 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,4023
Polymers14,3311
Non-polymers712
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.250, 79.250, 37.970
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-2018-

HOH

21A-2037-

HOH

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Components

#1: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / GAL D 4


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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 4.5
Details: LYSOZYME WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION CONTAINING 0.3% BETA-OCTYL- ...Details: LYSOZYME WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION CONTAINING 0.3% BETA-OCTYL-GLUCOSIDE (M/V) TO FACILITATE SAMPLE LOADING BY CAPILLARITY. CRYSTALLANT RESERVOIRS WERE FILLED WITH 1 M NACL CONTAINING 30% (M/V) PEG-3350 OR 2 M NACL, AND 0.1 M SODIUM ACETATE PH 4.5.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→30 Å / Num. obs: 22727 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.4
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IEE
Resolution: 1.43→27.415 Å / SU ML: 0.13 / σ(F): 3.28 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 1134 5 %
Rwork0.1685 --
obs0.1692 22684 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14 Å2
Refinement stepCycle: LAST / Resolution: 1.43→27.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 82 1085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041025
X-RAY DIFFRACTIONf_angle_d0.9371381
X-RAY DIFFRACTIONf_dihedral_angle_d12.364365
X-RAY DIFFRACTIONf_chiral_restr0.074144
X-RAY DIFFRACTIONf_plane_restr0.003181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4299-1.4950.24311370.21742584X-RAY DIFFRACTION97
1.495-1.57380.20011380.20812641X-RAY DIFFRACTION99
1.5738-1.67240.20621380.18352646X-RAY DIFFRACTION99
1.6724-1.80150.23051420.18422682X-RAY DIFFRACTION99
1.8015-1.98270.17371410.17382688X-RAY DIFFRACTION100
1.9827-2.26950.20431430.16562709X-RAY DIFFRACTION100
2.2695-2.85890.19911440.17682732X-RAY DIFFRACTION99
2.8589-27.42030.15441510.15292868X-RAY DIFFRACTION99

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