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- PDB-4ok7: Structure of bacteriophage SPN1S endolysin from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 4ok7
TitleStructure of bacteriophage SPN1S endolysin from Salmonella typhimurium
ComponentsEndolysin
KeywordsHYDROLASE / Helical protein
Function / homology: / Glycoside hydrolase, family 19, catalytic / Chitinase class I / chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / Lysozyme-like domain superfamily / hydrolase activity / Endolysin
Function and homology information
Biological speciesSalmonella phage SPN1S (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, Y. / Lim, J. / Kong, M. / Ryu, S. / Rhee, S.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structure of bacteriophage SPN1S endolysin reveals an unusual two-module fold for the peptidoglycan lytic and binding activity.
Authors: Park, Y. / Lim, J.A. / Kong, M. / Ryu, S. / Rhee, S.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Endolysin
B: Endolysin
C: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,52721
Polymers74,8143
Non-polymers1,71318
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5067
Polymers24,9381
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6028
Polymers24,9381
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4186
Polymers24,9381
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.616, 120.597, 126.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endolysin


Mass: 24937.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage SPN1S (virus) / Gene: SPC32N_026, SPN1S_0028 / Production host: Escherichia coli (E. coli) / References: UniProt: H2D0G4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.6 M ammonium sulfate and 0.1 M Na citrate, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 397049 / Num. obs: 64722 / % possible obs: 98.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.107 / Χ2: 1.08 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.976.20.58763020.629197
1.97-2.056.20.4463190.672197.3
2.05-2.146.20.30663670.737197.7
2.14-2.256.20.24964230.773198.1
2.25-2.396.20.19263890.855198.3
2.39-2.586.20.14964810.949198.5
2.58-2.846.20.12364721.093198.7
2.84-3.256.20.09465521.246198.9
3.25-4.096.10.06866001.645199
4.09-505.70.06468172.226197.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2363 6404 9.6 %
Rwork0.2079 --
all-66687 -
obs-63532 95.3 %
Solvent computationBsol: 55.3604 Å2
Displacement parametersBiso max: 102.67 Å2 / Biso mean: 24.8094 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--3.778 Å20 Å20 Å2
2--0.419 Å20 Å2
3---3.359 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 94 321 5680
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2381.5
X-RAY DIFFRACTIONc_scbond_it2.2212
X-RAY DIFFRACTIONc_mcangle_it1.8742
X-RAY DIFFRACTIONc_scangle_it3.1252.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6SO4.par
X-RAY DIFFRACTION7GOL.par

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