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

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Basic information

Entry
Database: PDB / ID: 6syd
TitleCrystal structure of the lysozyme in presence of bromophenol blue at pH 5.5
ComponentsLysozyme
KeywordsHYDROLASE / GLYCOSIDASE / Dye-soaking
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
bromophenol blue / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0243
Polymers14,3311
Non-polymers6932
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.498, 78.498, 37.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

21A-443-

HOH

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Components

#1: Protein Lysozyme


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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-LYE / bromophenol blue


Mass: 669.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H10Br4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, 0.3-0.5 sodium chloride at pH 4.6. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium ...Details: 0.1 M sodium acetate, 0.3-0.5 sodium chloride at pH 4.6. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium chloride, 0.1 M sodium acetate buffer at pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.1→19.04 Å / Num. obs: 89752 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 18.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.1-1.126.90.8931602823340.7690.3610.9661.7100
6.03-19.046.30.02620933310.9990.010.02853.994.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F1R

6f1r


Resolution: 1.1→19.04 Å / SU ML: 0.1122 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.2005
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
Rfree0.2324 4478 4.99 %
Rwork0.2067 85274 -
obs0.2079 89752 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.44 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 30 155 1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051056
X-RAY DIFFRACTIONf_angle_d0.70461434
X-RAY DIFFRACTIONf_chiral_restr0.0656145
X-RAY DIFFRACTIONf_plane_restr0.0036185
X-RAY DIFFRACTIONf_dihedral_angle_d16.229166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.30751650.29432833X-RAY DIFFRACTION99.73
1.11-1.130.29461610.29552855X-RAY DIFFRACTION99.41
1.13-1.140.31131790.28762810X-RAY DIFFRACTION99.47
1.14-1.150.27951510.27442845X-RAY DIFFRACTION99.4
1.15-1.170.29811850.27742838X-RAY DIFFRACTION99.41
1.17-1.180.29981730.2542824X-RAY DIFFRACTION99.67
1.18-1.20.25621670.25912827X-RAY DIFFRACTION99.57
1.2-1.220.27611680.24962853X-RAY DIFFRACTION99.6
1.22-1.240.25021100.24852880X-RAY DIFFRACTION99.4
1.24-1.260.22251470.252871X-RAY DIFFRACTION99.51
1.26-1.280.28031320.24212874X-RAY DIFFRACTION99.64
1.28-1.30.30751480.24232825X-RAY DIFFRACTION99.87
1.3-1.330.19431280.23432917X-RAY DIFFRACTION99.87
1.33-1.360.24931530.21972840X-RAY DIFFRACTION99.8
1.36-1.390.23991560.22812862X-RAY DIFFRACTION99.7
1.39-1.420.22511260.21962862X-RAY DIFFRACTION99.73
1.42-1.450.22971430.2132882X-RAY DIFFRACTION99.83
1.45-1.490.23521670.20992829X-RAY DIFFRACTION99.73
1.49-1.540.21171460.21432888X-RAY DIFFRACTION99.87
1.54-1.590.26821560.20842825X-RAY DIFFRACTION99.7
1.59-1.640.21951470.20792895X-RAY DIFFRACTION99.48
1.64-1.710.19831260.20332862X-RAY DIFFRACTION99.47
1.71-1.790.25651440.20962847X-RAY DIFFRACTION99.07
1.79-1.880.23681600.20922805X-RAY DIFFRACTION98.64
1.88-20.21621230.19932811X-RAY DIFFRACTION97.77
2-2.150.16991360.18462820X-RAY DIFFRACTION98.08
2.15-2.370.2431480.19362804X-RAY DIFFRACTION97.43
2.37-2.710.2291540.19812802X-RAY DIFFRACTION97.27
2.71-3.410.21081470.19672788X-RAY DIFFRACTION97.61
3.41-19.040.24411320.19712800X-RAY DIFFRACTION96.96

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