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- PDB-8anv: Crystal structure of phi3T_93 and phi3T AimX complex -

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Basic information

Entry
Database: PDB / ID: 8anv
TitleCrystal structure of phi3T_93 and phi3T AimX complex
Components
  • Arbitrium putative lysogeny regulator
  • YopN. Phi3T_93
KeywordsVIRAL PROTEIN / Arbitrium / Phi3T / lysis-lysogeny decission
Function / homologyArc-type ribbon-helix-helix / regulation of DNA-templated transcription / metal ion binding / NICKEL (II) ION / Uncharacterized protein / Arbitrium putative lysogeny regulator
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
DepositionAug 5, 2022Deposition 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
A: YopN. Phi3T_93
B: YopN. Phi3T_93
C: Arbitrium putative lysogeny regulator
F: Arbitrium putative lysogeny regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4106
Polymers31,3114
Non-polymers992
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.438, 66.438, 85.129
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-211-

HOH

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Components

#1: Protein YopN. Phi3T_93


Mass: 9768.052 Da / Num. of mol.: 2
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: Protein Arbitrium putative lysogeny regulator


Mass: 5887.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi3T (virus) / Gene: phi3T_91 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1P8CWW2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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

Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH7.5, 10%PEG8000, 0.2M Calcium acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→85.14 Å / Num. obs: 11446 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 51.3611068847 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.03 / Net I/σ(I): 7.4
Reflection shellResolution: 2.19→2.32 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1101 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.67 Å / SU ML: 0.2268 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 603 5.28 %
Rwork0.2273 10825 -
obs0.2277 11412 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 2 38 1370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871362
X-RAY DIFFRACTIONf_angle_d1.02171835
X-RAY DIFFRACTIONf_chiral_restr0.0605187
X-RAY DIFFRACTIONf_plane_restr0.0048234
X-RAY DIFFRACTIONf_dihedral_angle_d19.2259497
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.3208 37 -
Rwork0.3569 2623 -
obs--99.14 %
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)
14.309128674522.98720082957-4.183028657452.15336593257-2.868637847664.083694037430.126872658139-3.167753425110.1148078986152.655708879010.08186320361990.9905162725221.027439077751.31509552986-0.3610136792131.06258919992-0.02711397989080.05938843675891.154817814620.2642834227330.97202923705415.308684606815.690614640234.1396530747
26.573889948171.825047034290.1980022369736.91988136217-1.213100951214.39474802165-0.0403251596223-0.178545772051-0.5560914180960.596303238548-0.197207395993-0.02733121224770.179949471928-0.6391035548140.2381178008230.326385875905-0.007524630613390.04882981149660.4743571533183.7090570547E-50.50656328277317.79823892118.833700585317.5308141439
34.060747952952.857327192394.136229618848.91586260306-0.9086042842529.60383087194-0.375088892467-0.2191880568330.187035043136-0.371199507060.173742408674-0.718856562345-0.120449477809-0.8490147173620.2395011493940.319188123742-0.030536770934-0.01839866741240.5716397675620.04078863639430.58567879596626.973121357933.032746924612.2569190115
44.101886824445.905381268591.094628352629.76861349284-1.380052413156.682253555580.246647415154-0.0652530584802-1.078548502931.62553450751-0.799724478033-0.329947687668-0.316595667787-0.5997878384230.4259741594090.47522491682-0.0379426573024-0.08452750921420.764423748207-0.07314986480090.76329635279229.870268319633.73621126627.8035492556
54.92438211973.87689111285-3.926423482158.85042674703-2.847048207113.19715065697-0.493887777099-1.138395333040.0568222210189-0.0398712123254-0.318191818491-0.6807600176180.8564439743330.6093730167440.5858218803870.368471270590.0419156555172-0.06459589901960.669629630360.04350757750090.61542415555133.738472346425.959615084221.1665422076
61.65807828687-1.728587748842.065174180532.12905338753-2.637365327353.362763001120.835005138664-0.0323075841209-1.36630154539-2.391249550922.600447588450.7204126842121.58156127125-0.294175771903-3.190249142740.729104035852-0.132925736833-0.1429754767090.927252362931-0.07163993195341.5784669061132.274677068916.397336826517.0817021294
74.538559357241.616818684670.3591871044136.15893420771-2.654715335285.185643185140.255009676101-0.295151280337-1.12435922673-0.0593273916294-0.161259720946-0.138171948170.8563291585320.0758791023765-0.06448473433120.353615522928-0.0309840080831-0.07423827053360.4808132594370.02154019354540.65631904375524.087495481616.660362427722.2508385099
89.089910970583.801224037595.992535478238.349211184834.843281063158.95076644963-0.163600437003-0.1382118041370.605414986026-0.350073723929-0.0348720545561-0.367033695758-0.629117442416-0.6241066868620.1465778326210.2665397306130.04650043380190.05379944616810.4370599748880.001304145957430.5480029672713.181313089530.42064254619.99483955876
92.91430520451-1.189450304041.286654259755.59481241468-3.951911975232.89855403670.1272727237040.288494116799-1.31055466921-0.7376836418690.007776677701130.05774980404372.04487614291-0.192230737459-0.1499045556520.557523595541-0.07066873280940.007963709161040.403353477003-0.084750277660.688062011813.127036612114.84790986426.40347916798
102.22623100589-2.2578110593.198499701029.002568042180.673766884822.993465158150.100062096489-0.725472667911-1.06643581870.176128757748-0.05025377483580.6655823384310.43510959601-0.7638452134180.01872279624030.394662778681-0.02337568695190.06668543124770.7039576418920.05855972299610.6838194512857.8615967008121.782630492718.3467404961
115.38701014374.9079786929-1.832962529345.274295204540.9254843857919.050401318620.629924709852-1.679211611690.7429568665021.32982760125-0.6860900522121.14206614949-0.541800064302-0.484234438881-0.01060942032640.700572998048-0.09423176556850.1122651038480.9339973088030.006639142373380.63821314535817.965195882124.790747489331.5465615475
123.041470513791.89300172961-1.61836649875.614127165394.062681081576.922547885610.9883431430641.34735041308-1.01584669828-0.455093602645-0.4113730601270.1872724584310.1788241077330.216193792309-0.6281538008620.6660841008810.152134883413-0.2247706928280.6089522780740.1478193489030.90099303435922.658418958610.459803224313.3543429034
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 8 )AA2 - 81 - 7
22chain 'A' and (resid 9 through 26 )AA9 - 268 - 25
33chain 'A' and (resid 27 through 41 )AA27 - 4126 - 40
44chain 'A' and (resid 42 through 51 )AA42 - 5141 - 50
55chain 'A' and (resid 52 through 60 )AA52 - 6051 - 59
66chain 'A' and (resid 61 through 67 )AA61 - 6760 - 66
77chain 'B' and (resid 1 through 26 )BB1 - 261 - 26
88chain 'B' and (resid 27 through 44 )BB27 - 4427 - 44
99chain 'B' and (resid 45 through 51 )BB45 - 5145 - 51
1010chain 'B' and (resid 52 through 67 )BB52 - 6752 - 67
1111chain 'C' and (resid 9 through 22 )CE9 - 221 - 14
1212chain 'F' and (resid 10 through 22 )FF10 - 221 - 13

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