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- PDB-8hp8: Crystal Structure of Engineered Endolysin EC340 derived from Gram... -

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Basic information

Entry
Database: PDB / ID: 8hp8
TitleCrystal Structure of Engineered Endolysin EC340 derived from Gram-Negative Bacteria targeted Bacteriophage
ComponentsEndolysin mtEC340M
KeywordsHYDROLASE / Endolysin / Gram-Negative Bacteria / Bacteriophage / VIRAL PROTEIN
Function / homologyLysozyme - #40 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia phage PBEC131 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.397 Å
AuthorsWang, J.M. / Yoon, W.S. / Seo, M.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C300888911 Korea, Republic Of
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of the engineered endolysin mtEC340M.
Authors: Wang, J.M. / Seok, S.H. / Yoon, W.S. / Kim, J.H. / Seo, M.D.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin mtEC340M
B: Endolysin mtEC340M
C: Endolysin mtEC340M


Theoretical massNumber of molelcules
Total (without water)51,0163
Polymers51,0163
Non-polymers00
Water5,513306
1
A: Endolysin mtEC340M


Theoretical massNumber of molelcules
Total (without water)17,0051
Polymers17,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin mtEC340M


Theoretical massNumber of molelcules
Total (without water)17,0051
Polymers17,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endolysin mtEC340M


Theoretical massNumber of molelcules
Total (without water)17,0051
Polymers17,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.700, 125.042, 69.237
Angle α, β, γ (deg.)90.00, 114.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

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Components

#1: Protein Endolysin mtEC340M


Mass: 17005.398 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage PBEC131 (virus) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M citrate, pH 5.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.397→34.78 Å / Num. obs: 24857 / % possible obs: 98.3 % / Redundancy: 6.8 % / CC1/2: 0.975 / Net I/σ(I): 25.3529
Reflection shellResolution: 2.4→6.54 Å / Num. unique obs: 1197 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
PHENIX(1.14_3260)phasing
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.397→34.78 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1964 8.09 %
Rwork0.1758 --
obs0.1807 24290 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 0 306 3886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073643
X-RAY DIFFRACTIONf_angle_d0.8144927
X-RAY DIFFRACTIONf_dihedral_angle_d2.7192161
X-RAY DIFFRACTIONf_chiral_restr0.043554
X-RAY DIFFRACTIONf_plane_restr0.006646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.45570.3651210.23131432X-RAY DIFFRACTION86
2.4557-2.5220.30571380.21561550X-RAY DIFFRACTION94
2.522-2.59620.29011400.19831585X-RAY DIFFRACTION94
2.5962-2.680.26241400.19781584X-RAY DIFFRACTION96
2.68-2.77570.2761440.19391599X-RAY DIFFRACTION96
2.7757-2.88680.27021410.19921595X-RAY DIFFRACTION96
2.8868-3.01810.27791410.20921611X-RAY DIFFRACTION98
3.0181-3.17720.25191440.2041628X-RAY DIFFRACTION98
3.1772-3.37610.25251440.19661637X-RAY DIFFRACTION98
3.3761-3.63650.24331410.17821603X-RAY DIFFRACTION96
3.6365-4.00190.24151440.16211640X-RAY DIFFRACTION98
4.0019-4.57990.22211410.14551605X-RAY DIFFRACTION97
4.5799-5.7660.16881450.14431651X-RAY DIFFRACTION98
5.766-6.540.1681400.1551606X-RAY DIFFRACTION94

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