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- PDB-6ilu: Endolysin LysPBC5 CBD -

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Basic information

Entry
Database: PDB / ID: 6ilu
TitleEndolysin LysPBC5 CBD
ComponentsLysin
KeywordsSUGAR BINDING PROTEIN / cell-wall binding / endolysin / PBC5 / SH3b
Function / homologyGlycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / Glycoside hydrolase superfamily / Lysozyme
Function and homology information
Biological speciesBacillus phage PBC5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 Å
AuthorsSuh, J.Y. / Ryu, K.S. / Ryu, S. / Lee, K.O. / Kong, M.S. / Bae, J.W. / Kim, I.T.
CitationJournal: Structure / Year: 2019
Title: Structural Basis for Cell-Wall Recognition by Bacteriophage PBC5 Endolysin.
Authors: Lee, K.O. / Kong, M. / Kim, I. / Bai, J. / Cha, S. / Kim, B. / Ryu, K.S. / Ryu, S. / Suh, J.Y.
History
DepositionOct 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Mar 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

Downloads & links

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Assembly

Deposited unit
A: Lysin
B: Lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,55222
Polymers31,0392
Non-polymers1,51320
Water8,503472
1
A: Lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,31011
Polymers15,5191
Non-polymers79110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area7350 Å2
MethodPISA
2
B: Lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,24211
Polymers15,5191
Non-polymers72310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.823, 107.514, 117.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Lysin /


Mass: 15519.267 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBC5 (virus) / Gene: PBC5_032 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A218KCJ1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 4.16 Å3/Da / Density % sol: 70.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.601→50 Å / Num. obs: 65554 / % possible obs: 95.96 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 54.58
Reflection shellResolution: 1.601→1.641 Å / Rmerge(I) obs: 0.337 / Num. unique obs: 5078

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.601→36.361 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 18.68
RfactorNum. reflection% reflection
Rfree0.1963 2000 3.05 %
Rwork0.1671 --
obs0.168 65554 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→36.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 88 472 2698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152276
X-RAY DIFFRACTIONf_angle_d1.4543072
X-RAY DIFFRACTIONf_dihedral_angle_d11.554790
X-RAY DIFFRACTIONf_chiral_restr0.083288
X-RAY DIFFRACTIONf_plane_restr0.009390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6012-1.64120.27161030.28563262X-RAY DIFFRACTION70
1.6412-1.68560.27961230.25453938X-RAY DIFFRACTION84
1.6856-1.73520.24911360.22714317X-RAY DIFFRACTION92
1.7352-1.79120.21431480.20634666X-RAY DIFFRACTION99
1.7912-1.85520.20041460.18214658X-RAY DIFFRACTION100
1.8552-1.92950.20441470.16314671X-RAY DIFFRACTION100
1.9295-2.01730.16121480.15034684X-RAY DIFFRACTION100
2.0173-2.12370.17831480.14884710X-RAY DIFFRACTION100
2.1237-2.25670.15991470.15294687X-RAY DIFFRACTION100
2.2567-2.43090.20041490.15714736X-RAY DIFFRACTION100
2.4309-2.67550.23041490.16954733X-RAY DIFFRACTION100
2.6755-3.06240.21041500.17674763X-RAY DIFFRACTION100
3.0624-3.85770.18721510.1524806X-RAY DIFFRACTION100
3.8577-36.370.18161550.16014923X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.16430.4097-6.13132.1054-0.41779.7104-0.1646-0.0485-0.481-0.1863-0.04640.59230.5475-0.68750.07570.17750.00860.00970.29180.03290.334121.18699.337741.8782
21.6308-0.73231.89942.16290.09915.94920.18190.0316-0.1272-0.4389-0.04650.31520.2497-0.4615-0.08410.27690.0591-0.13020.23740.02710.281618.929211.842719.6018
33.09723.12823.06295.26481.45114.5903-0.10350.5393-0.2647-0.62790.2195-0.17550.07120.2743-0.11210.3240.0652-0.02940.24180.00310.177935.30557.932421.1676
46.03360.08650.32511.1087-0.1241.8940.05740.2984-0.3287-0.34730.05680.29950.1226-0.1936-0.10960.24240.0507-0.08930.18620.03390.252525.01246.830224.3799
57.8092-0.62321.6379.8057-4.03512.17080.13970.64330.805-0.8616-0.5263-0.1115-0.56260.18430.19040.3230.0536-0.00510.29330.0470.296334.623419.452426.0716
63.9112-0.0442-0.34311.6034-0.05373.85720.16150.1186-0.0781-0.4411-0.03370.24170.0064-0.0532-0.12090.20890.0668-0.07160.18170.02620.212928.096811.637626.3804
71.52520.75291.03522.17760.79722.3538-0.0187-0.17480.00060.063-0.06240.1834-0.1932-0.20620.0980.17380.04370.05980.19670.01120.192829.371820.290349.4714
85.7256-0.89451.31183.57142.7714.3034-0.0875-0.33230.381-0.1664-0.16880.3434-0.415-0.44050.2540.18320.03770.04470.16240.040.182329.782124.493745.6144
91.00510.56811.23435.7878-0.6535.46670.1450.0396-0.1062-0.1669-0.1569-0.0995-0.05680.32720.00830.15490.05250.0330.22190.03030.196132.706915.859442.5617
104.55352.4210.51664.28231.65175.23640.0479-0.24040.16450.1474-0.14450.44830.0601-0.45820.10540.15860.05260.04990.20360.02020.204725.695215.800846.8289
111.20291.64130.1173.17981.72162.5330.1879-0.0558-0.05520.47990.0148-0.576-0.0610.3971-0.19920.2028-0.02550.02030.29110.01910.299861.947224.494947.9459
123.11451.32463.53743.8691.4336.59090.198-0.62820.38690.1393-0.2480.3521-0.3151-0.63570.0180.2433-0.00030.0970.20940.0050.181246.244530.547752.3807
135.2574-0.0089-0.21732.40940.94181.28890.1236-0.27850.03280.2365-0.02-0.226-0.05580.1481-0.0980.2384-0.04980.03610.21430.05230.186556.310826.733752.8721
144.3302-1.89151.68083.1021.73597.95130.24410.16830.07470.0528-0.08990.2291-0.0912-0.3206-0.19170.1876-0.04050.08040.20250.03930.206449.317726.05947.2877
156.05211.2186-1.98394.97791.02633.99740.37870.14220.0319-0.0557-0.1605-0.3419-0.47010.2256-0.20120.1784-0.02580.04620.18270.03850.174455.880228.155644.7734
161.71870.07481.29122.33550.00871.30260.04880.0646-0.1374-0.26940.0479-0.1885-0.0210.1767-0.10780.17380.05080.05010.1948-0.01770.185252.19157.194932.1039
172.99270.04490.51182.74532.84023.29390.08620.2457-0.0659-0.49330.1296-0.3517-0.33270.3689-0.21540.27690.04560.07830.20420.03280.176851.887812.100729.3605
181.08311.15760.56975.7011-1.61074.71720.1108-0.05670.08420.0110.07250.3304-0.2873-0.1936-0.20680.13210.04050.04020.18350.0090.17948.756812.495338.3837
194.14570.24374.12113.99332.07896.4970.06860.2743-0.21170.03810.187-0.5670.23730.4386-0.2560.15240.04680.05290.1649-0.00370.216155.71018.247737.318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 205 through 211 )
2X-RAY DIFFRACTION2chain 'A' and (resid 212 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 251 )
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 257 )
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 278 )
7X-RAY DIFFRACTION7chain 'A' and (resid 279 through 300 )
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 314 )
9X-RAY DIFFRACTION9chain 'A' and (resid 315 through 327 )
10X-RAY DIFFRACTION10chain 'A' and (resid 328 through 339 )
11X-RAY DIFFRACTION11chain 'B' and (resid 205 through 223 )
12X-RAY DIFFRACTION12chain 'B' and (resid 224 through 233 )
13X-RAY DIFFRACTION13chain 'B' and (resid 234 through 251 )
14X-RAY DIFFRACTION14chain 'B' and (resid 252 through 267 )
15X-RAY DIFFRACTION15chain 'B' and (resid 268 through 278 )
16X-RAY DIFFRACTION16chain 'B' and (resid 279 through 300 )
17X-RAY DIFFRACTION17chain 'B' and (resid 301 through 314 )
18X-RAY DIFFRACTION18chain 'B' and (resid 315 through 327 )
19X-RAY DIFFRACTION19chain 'B' and (resid 328 through 339 )

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