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- PDB-6ist: Crystal structure of a wild type endolysin LysIME-EF1 -

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Basic information

Entry
Database: PDB / ID: 6ist
TitleCrystal structure of a wild type endolysin LysIME-EF1
Components(Lysin) x 2
KeywordsHYDROLASE / Lysin
Function / homologyCHAP domain profile. / CHAP domain / CHAP domain / symbiont-mediated cytolysis of host cell / Papain-like cysteine peptidase superfamily / metal ion binding / Lysin
Function and homology information
Biological speciesEnterococcus phage IMEEF1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsOuyang, S.Y.
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage.
Authors: Zhou, B. / Zhen, X. / Zhou, H. / Zhao, F. / Fan, C. / Perculija, V. / Tong, Y. / Mi, Z. / Ouyang, S.
History
DepositionNov 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Feb 19, 2020Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.3Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Lysin
B: Lysin
C: Lysin
D: Lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8165
Polymers50,7764
Non-polymers401
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-61 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 56.920, 91.520
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysin


Mass: 8166.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus phage IMEEF1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: S5MRN1
#2: Protein Lysin


Mass: 26276.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus phage IMEEF1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: S5MRN1
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 3350 0.1M Tris ,pH 8.5 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 1.75→90.97 Å / Num. obs: 47634 / % possible obs: 98 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.173 / Net I/σ(I): 2
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 3471 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.75→90.97 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.536 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22349 2000 4.2 %RANDOM
Rwork0.18017 ---
obs0.18198 45621 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.578 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→90.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 1 393 3783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023478
X-RAY DIFFRACTIONr_bond_other_d0.0020.023277
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9334705
X-RAY DIFFRACTIONr_angle_other_deg1.02437499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80723.963164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05215585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1321518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5732.5951690
X-RAY DIFFRACTIONr_mcbond_other2.5722.5911689
X-RAY DIFFRACTIONr_mcangle_it3.7673.8632102
X-RAY DIFFRACTIONr_mcangle_other3.7663.8672103
X-RAY DIFFRACTIONr_scbond_it3.6653.0271788
X-RAY DIFFRACTIONr_scbond_other3.6643.0311789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5984.3632604
X-RAY DIFFRACTIONr_long_range_B_refined7.69322.7184317
X-RAY DIFFRACTIONr_long_range_B_other7.52922.1214160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 146 -
Rwork0.325 3325 -
obs--97.04 %

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