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- PDB-6sye: Crystal structure of orthorhombic lysozyme in presence of the dye... -

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Basic information

Entry
Database: PDB / ID: 6sye
TitleCrystal structure of orthorhombic lysozyme in presence of the dye bromophenol blue at pH 7.0
ComponentsLysozyme C
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
bromophenol blue / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.97 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7074
Polymers14,3311
Non-polymers1,3753
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.206, 55.235, 71.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LYE / bromophenol blue / Bromophenol blue


Mass: 669.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H10Br4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.96 % / Mosaicity: 0.26 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals grew in 0.1 M sodium acetate, 0.3 M sodium chloride at pH 4.6 in the presence of 0.1 M Lithium sulfate. After growth, and before measurement, these crystals were soaked in the dye ...Details: Crystals grew in 0.1 M sodium acetate, 0.3 M sodium chloride at pH 4.6 in the presence of 0.1 M Lithium sulfate. After growth, and before measurement, these crystals were soaked in the dye solution: saturated bromophenol blue, 0.3 M sodium chloride, 100 mM Lithium sulfate, 100 mM phosphate buffer at pH 7.0

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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 PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 0.97→19.6 Å / Num. obs: 137004 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 10.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.013 / Rrim(I) all: 0.033 / Net I/σ(I): 23.7
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
0.97-0.984.50.9161559135000.6180.4841.0391.698.3
5.29-19.65.60.02228685120.9990.010.02472.297.4

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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: 0.97→19.6 Å / SU ML: 0.0969 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 19.7886
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
Rfree0.1983 6932 5.06 %
Rwork0.1731 130072 -
obs0.1744 137004 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.21 Å2
Refinement stepCycle: LAST / Resolution: 0.97→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 59 160 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931110
X-RAY DIFFRACTIONf_angle_d1.05611514
X-RAY DIFFRACTIONf_chiral_restr0.0768150
X-RAY DIFFRACTIONf_plane_restr0.0055193
X-RAY DIFFRACTIONf_dihedral_angle_d21.733423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.36552330.30334177X-RAY DIFFRACTION95.25
0.98-0.990.29772380.27684284X-RAY DIFFRACTION98.52
0.99-10.28542650.26054297X-RAY DIFFRACTION97.94
1-1.010.28811980.24294319X-RAY DIFFRACTION97.98
1.01-1.030.23692140.23764356X-RAY DIFFRACTION99.15
1.03-1.040.24462490.22654382X-RAY DIFFRACTION98.91
1.04-1.060.24422200.214293X-RAY DIFFRACTION99.51
1.06-1.070.21552060.19614402X-RAY DIFFRACTION99.25
1.07-1.090.22952190.18794380X-RAY DIFFRACTION99.2
1.09-1.110.2152450.18044334X-RAY DIFFRACTION99.09
1.11-1.130.17472150.17394379X-RAY DIFFRACTION99.24
1.13-1.150.19962330.16614307X-RAY DIFFRACTION99.1
1.15-1.170.18762550.16664371X-RAY DIFFRACTION99.1
1.17-1.190.14932380.15934310X-RAY DIFFRACTION99.43
1.19-1.220.16972260.16414355X-RAY DIFFRACTION99.31
1.22-1.250.17762190.17064359X-RAY DIFFRACTION99.54
1.25-1.280.21582400.17014364X-RAY DIFFRACTION99.2
1.28-1.310.19092260.16974401X-RAY DIFFRACTION99.42
1.31-1.350.19272650.17654269X-RAY DIFFRACTION99.32
1.35-1.390.19292470.17524356X-RAY DIFFRACTION99.52
1.39-1.440.20882200.16614402X-RAY DIFFRACTION99.57
1.44-1.50.18242030.16564378X-RAY DIFFRACTION99.46
1.5-1.570.16941960.16624396X-RAY DIFFRACTION99.5
1.57-1.650.18532220.16264345X-RAY DIFFRACTION99.24
1.65-1.760.18912610.16814316X-RAY DIFFRACTION98.43
1.76-1.890.17511930.17034349X-RAY DIFFRACTION98.52
1.89-2.080.18782390.16454280X-RAY DIFFRACTION98.35
2.08-2.380.19752570.16754306X-RAY DIFFRACTION98.49
2.38-30.18332090.16734346X-RAY DIFFRACTION98.32
3-19.60.21342810.17264259X-RAY DIFFRACTION98.57

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