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- PDB-8c8e: Crystal structure of phi3T_93 L23D mutant -

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Basic information

Entry
Database: PDB / ID: 8c8e
TitleCrystal structure of phi3T_93 L23D mutant
ComponentsPhi3T YopN
KeywordsVIRAL PROTEIN / arbitrium / quorum sensing
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesBacillus phage phi3T (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZamora-Caballero, S. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-108541GB-100 Spain
CitationJournal: Nat Microbiol / Year: 2024
Title: Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision.
Authors: Zamora-Caballero, S. / Chmielowska, C. / Quiles-Puchalt, N. / Brady, A. / Del Sol, F.G. / Mancheno-Bonillo, J. / Felipe-Ruiz, A. / Meijer, W.J.J. / Penades, J.R. / Marina, A.
History
DepositionJan 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Phi3T YopN
A: Phi3T YopN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5803
Polymers19,5402
Non-polymers401
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-40 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.890, 71.890, 68.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

CA

21A-210-

HOH

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Components

#1: Protein Phi3T YopN


Mass: 9769.981 Da / Num. of mol.: 2 / Mutation: L23D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi3T (virus) / Gene: phi3T_93 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1P8CWW1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% w/vPEG 8000, 100mM HEPES Sodium Salt, 200mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2022
RadiationMonochromator: Channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.199→62.26 Å / Num. obs: 10758 / % possible obs: 100 % / Redundancy: 16.7 % / Biso Wilson estimate: 40.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.041 / Rrim(I) all: 0.124 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.119 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 912 / CC1/2: 0.904 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459phasing
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→62.26 Å / SU ML: 0.2578 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 536 5 %
Rwork0.2097 10189 -
obs0.2112 10725 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 1 28 1149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751159
X-RAY DIFFRACTIONf_angle_d0.89191571
X-RAY DIFFRACTIONf_chiral_restr0.0534161
X-RAY DIFFRACTIONf_plane_restr0.0069204
X-RAY DIFFRACTIONf_dihedral_angle_d17.6901415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.28391320.27092499X-RAY DIFFRACTION99.85
2.42-2.770.31521240.2262518X-RAY DIFFRACTION99.92
2.77-3.490.24771190.2392549X-RAY DIFFRACTION99.89
3.49-62.260.21431610.18362623X-RAY DIFFRACTION99.96
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.88347191991-1.167218627211.781887813124.26974259049-3.235758440145.132797070550.0774452066655-1.17212491221-0.2945399149532.25657832910.2638681493410.993880321350.0213680106858-1.19205523704-0.3285642313461.25344989981-0.09138353741460.1846769778720.7847091041190.1818509003180.77737715203838.799516796215.007689983517.2307244759
25.348297847050.09566109576483.063153671950.924429802871-0.0007528597472149.064550089250.252578020846-0.295511352361-0.8643622154880.967248341769-0.00567159292768-0.6120709983690.08730781732480.534249743522-0.1021381451980.644275798189-0.122244143492-0.2012089971820.3409138774630.09003856857760.57709498212646.49749572866.558079938236.61890105458
37.40752738136-0.819242737927-0.5418329621194.087702844196.271006014749.68498435361-0.4360188095050.380551574383-0.341035966318-0.1115653634230.0599459124777-0.232739655365-0.103201306670.6190679379970.2996265470060.471755088893-0.1189345830440.03067521409120.3699570020530.07117797116790.39525335343146.19702188718.4039729784-6.50744428145
47.114038451761.63080544641-2.362554309057.630784518531.846002885717.24137060160.209434057071-1.00257534214-1.196294064850.0225165576021-0.283833310745-0.592196664175-0.09367940565710.7876262762090.04125583214850.362754145069-0.120098896788-0.03921961201990.4365710028640.07317299410840.48223033906549.698801361321.94005395664.12688918113
50.725920702007-0.9040597865212.168383937391.96408619074-3.279517770976.882065324830.343638489875-0.42041007874-0.6238854992670.2155709910850.262911385818-1.47902998651.79335178321.15747828056-0.2913957250061.307598815420.13676148572-0.7358812283570.7756340128580.1175681400491.7753681224256.8300203346.0387724288612.0791432303
62.446300388030.8325483024990.8184204869713.696687383991.679789815383.583204322560.434393097927-0.223254348426-0.623964552430.777725920498-0.168510678221-0.3278280752110.449701484394-0.0379047966965-0.2707937225490.521650684147-0.127187608564-0.1225355912390.3453601504240.06676707923130.4756183638141.89350137755.726710692272.76735075352
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 0 through 8 )CA0 - 81 - 9
22chain 'C' and (resid 9 through 26 )CA9 - 2610 - 27
33chain 'C' and (resid 27 through 44 )CA27 - 4428 - 45
44chain 'C' and (resid 45 through 67 )CA45 - 6746 - 68
55chain 'A' and (resid 0 through 8 )AB0 - 81 - 9
66chain 'A' and (resid 9 through 67 )AB9 - 6710 - 68

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