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- PDB-6rt3: Native tetragonal lysozyme - synchrotron data -

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Basic information

Entry
Database: PDB / ID: 6rt3
TitleNative tetragonal lysozyme - synchrotron data
ComponentsLysozyme C
KeywordsHYDROLASE / Glycoside hydrolase
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: 1.05 Å
AuthorsPereira, P.J.B.
CitationJournal: Phys Chem Chem Phys / Year: 2020
Title: Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions.
Authors: Ferreira, C. / Pinto, M.F. / Macedo-Ribeiro, S. / Pereira, P.J.B. / Rocha, F.A. / Martins, P.M.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 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

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,07217
Polymers14,3311
Non-polymers74116
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-69 kcal/mol
Surface area6590 Å2
Unit cell
Length a, b, c (Å)78.863, 78.863, 36.800
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-359-

HOH

21A-469-

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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Acetate pH 4.8, 10% (w/v) NaCl, 25% (v/v) Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.05→39.43 Å / Num. obs: 53373 / % possible obs: 97.6 % / Redundancy: 10 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.017 / Rrim(I) all: 0.064 / Net I/σ(I): 11.4
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 1955 / % possible all: 73.8

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1X

2w1x


Resolution: 1.05→22.224 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.07
RfactorNum. reflection% reflection
Rfree0.1472 2644 4.98 %
Rwork0.1259 --
obs0.1269 53109 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.05→22.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 37 177 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051161
X-RAY DIFFRACTIONf_angle_d0.821566
X-RAY DIFFRACTIONf_dihedral_angle_d22.396445
X-RAY DIFFRACTIONf_chiral_restr0.076157
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.06910.4243920.41141815X-RAY DIFFRACTION68
1.0691-1.08970.31911220.34472330X-RAY DIFFRACTION86
1.0897-1.11190.2841330.30452578X-RAY DIFFRACTION96
1.1119-1.13610.29511540.26472649X-RAY DIFFRACTION100
1.1361-1.16250.25541660.2132654X-RAY DIFFRACTION99
1.1625-1.19160.17571350.16092700X-RAY DIFFRACTION100
1.1916-1.22380.13841300.12862704X-RAY DIFFRACTION100
1.2238-1.25980.14091190.1252707X-RAY DIFFRACTION100
1.2598-1.30050.16481510.1222683X-RAY DIFFRACTION100
1.3005-1.34690.14341440.1222705X-RAY DIFFRACTION100
1.3469-1.40090.13361300.10232729X-RAY DIFFRACTION100
1.4009-1.46460.12081460.08862707X-RAY DIFFRACTION100
1.4646-1.54180.11731330.08792748X-RAY DIFFRACTION100
1.5418-1.63840.1111490.08562723X-RAY DIFFRACTION100
1.6384-1.76480.11211480.09232735X-RAY DIFFRACTION100
1.7648-1.94230.11261320.09412761X-RAY DIFFRACTION100
1.9423-2.22320.11521480.09662772X-RAY DIFFRACTION100
2.2232-2.80010.13121470.11372820X-RAY DIFFRACTION100
2.8001-22.22880.16311650.14142945X-RAY DIFFRACTION100

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