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- PDB-6syc: Crystal structure of the lysozyme in presence of bromophenol blue... -

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Basic information

Entry
Database: PDB / ID: 6syc
TitleCrystal structure of the lysozyme in presence of bromophenol blue at pH 6.5
ComponentsLysozyme
KeywordsHYDROLASE / GLYCOSIDASE / Dye-soaking
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
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
IMIDAZOLE / bromophenol blue / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsCamara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Lysozyme crystals dyed with bromophenol blue: where has the dye gone?
Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Alba-Elena, D. / Martinez, J.C. / Camara-Artigas, A.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,17314
Polymers28,6622
Non-polymers5,51012
Water3,729207
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7635
Polymers14,3311
Non-polymers1,4324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4099
Polymers14,3311
Non-polymers4,0788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.719, 76.559, 84.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 219 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-LYE / bromophenol blue / Bromophenol blue


Mass: 669.961 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H10Br4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.92 % / Mosaicity: 0.53 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.3 M sodium chloride, 0.1 M imidazole. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium chloride, 0.1 M imidazole buffer at pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.38→19.395 Å / Num. obs: 90196 / % possible obs: 97.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.055 / Rrim(I) all: 0.115 / Net I/σ(I): 7.3
Reflection shellResolution: 1.38→1.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.397 / Num. measured all: 7286 / Num. unique obs: 2490 / CC1/2: 0.797 / Rpim(I) all: 0.271 / Rrim(I) all: 0.484 / Net I/σ(I) obs: 1.8 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F1M

6f1m


Resolution: 1.38→19.39 Å / SU ML: 0.1376 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.5892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The ligand geometry validation is not accurate because the molecule is a resonant form.
RfactorNum. reflection% reflection
Rfree0.2261 4572 5.07 %
Rwork0.191 85624 -
obs0.1928 90196 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.47 Å2
Refinement stepCycle: LAST / Resolution: 1.38→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 240 207 2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722294
X-RAY DIFFRACTIONf_angle_d0.89653142
X-RAY DIFFRACTIONf_chiral_restr0.0666295
X-RAY DIFFRACTIONf_plane_restr0.0045387
X-RAY DIFFRACTIONf_dihedral_angle_d25.037453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.30171300.24292817X-RAY DIFFRACTION90.57
1.4-1.420.25581470.22412670X-RAY DIFFRACTION89.03
1.42-1.430.25721490.2142719X-RAY DIFFRACTION89.4
1.43-1.450.25891800.22222899X-RAY DIFFRACTION94.71
1.45-1.470.25691560.2032899X-RAY DIFFRACTION97.29
1.47-1.490.23421430.20032919X-RAY DIFFRACTION96.17
1.49-1.510.26541330.19233001X-RAY DIFFRACTION96.4
1.51-1.530.23211620.1992888X-RAY DIFFRACTION95.58
1.53-1.560.24971380.19472994X-RAY DIFFRACTION97.45
1.56-1.580.23011430.18942924X-RAY DIFFRACTION97.09
1.58-1.610.24241790.18862907X-RAY DIFFRACTION96.95
1.61-1.640.21421570.18322986X-RAY DIFFRACTION96.71
1.64-1.670.24031540.1832773X-RAY DIFFRACTION93.34
1.67-1.710.2411360.17973023X-RAY DIFFRACTION96.81
1.71-1.740.21041650.17052907X-RAY DIFFRACTION97.77
1.74-1.780.21681410.17343016X-RAY DIFFRACTION98.41
1.78-1.830.22591550.17682943X-RAY DIFFRACTION97.88
1.83-1.880.23451620.17262983X-RAY DIFFRACTION97.64
1.88-1.930.24921380.17772898X-RAY DIFFRACTION95.92
1.93-20.19671820.17092917X-RAY DIFFRACTION95.77
2-2.060.21641420.17222353X-RAY DIFFRACTION89.04
2.08-2.150.22751230.17322188X-RAY DIFFRACTION92
2.15-2.250.24581490.17912941X-RAY DIFFRACTION96.05
2.25-2.370.19651600.17512949X-RAY DIFFRACTION97.16
2.37-2.510.19361750.18682904X-RAY DIFFRACTION96.01
2.51-2.710.22021670.18482875X-RAY DIFFRACTION95.75
2.71-2.980.22441480.19112788X-RAY DIFFRACTION91.66
2.98-3.410.27091430.1872835X-RAY DIFFRACTION93.41
3.41-4.280.18941520.19452896X-RAY DIFFRACTION95.16
4.29-19.390.23881630.22852812X-RAY DIFFRACTION93.29

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