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- PDB-6akv: Crystal structure of LysB4, the endolysin from Bacillus cereus-ta... -

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Basic information

Entry
Database: PDB / ID: 6akv
TitleCrystal structure of LysB4, the endolysin from Bacillus cereus-targeting bacteriophage B4
ComponentsLysB4
KeywordsHYDROLASE / endolysin / LAS type enzyme / L-Alanoyl D-Glutamate endopeptidase
Function / homology
Function and homology information


peptidoglycan stem peptide endopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M15C / D-alanyl-D-alanine carboxypeptidase / Bacterial SH3 domain / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage B4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHong, S. / Ha, N.-C.
CitationJournal: Mol. Cells / Year: 2019
Title: Crystal Structure of LysB4, an Endolysin fromBacillus cereus-Targeting Bacteriophage B4.
Authors: Hong, S. / Son, B. / Ryu, S. / Ha, N.C.
History
DepositionSep 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: LysB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2804
Polymers30,0831
Non-polymers1973
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-61 kcal/mol
Surface area7880 Å2
Unit cell
Length a, b, c (Å)79.457, 79.457, 77.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein LysB4 / Endolysin


Mass: 30083.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage B4 (virus) / Gene: lysB4, BCB4_0006 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: H9NAL3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 2% polyethylene glycol monomethyl ether 550 (PEGMME 550), 8 mM Tris(2-carboxyethyl)phosphine (TCEP)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8863 / % possible obs: 91.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 19.66
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 449 / CC1/2: 0.353 / Rpim(I) all: 0.222 / Rrim(I) all: 0.419 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VO9

2vo9


Resolution: 2.4→28.092 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 22.2
RfactorNum. reflection% reflection
Rfree0.2243 769 9.7 %
Rwork0.1756 --
obs0.1805 7926 81.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 7 23 1190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071188
X-RAY DIFFRACTIONf_angle_d0.7851606
X-RAY DIFFRACTIONf_dihedral_angle_d10.211692
X-RAY DIFFRACTIONf_chiral_restr0.047169
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.57150.28341080.2172890X-RAY DIFFRACTION52
2.5715-2.83010.28591620.2261576X-RAY DIFFRACTION91
2.8301-3.23910.28641830.20131728X-RAY DIFFRACTION99
3.2391-4.07890.20071200.17811194X-RAY DIFFRACTION68
4.0789-28.0920.18021960.14021769X-RAY DIFFRACTION99

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