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- PDB-7r6r: Crystal Structure of a Mycobacteriophage Cluster A2 Immunity Repr... -

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Basic information

Entry
Database: PDB / ID: 7r6r
TitleCrystal Structure of a Mycobacteriophage Cluster A2 Immunity Repressor:DNA Complex
Components
  • DNA (5'-D(P*CP*CP*CP*GP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*GP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*CP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*CP*GP*GP*G)-3')
  • Immunity repressor
KeywordsGENE REGULATION/DNA / Immunity repressor / helix-turn-helix motif / DNA binding protein / GENE REGULATION / GENE REGULATION-DNA complex
Function / homologyDNA / DNA (> 10) / Immunity repressor
Function and homology information
Biological speciesMycobacterium phage TipsytheTRex (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsMcGinnis, R.J. / Brambley, C.A. / Stamey, B. / Green, W.C. / Gragg, K.N. / Cafferty, E.R. / Terwilliger, T.C. / Hammel, M. / Hollis, T.J. / Miller, J.M. ...McGinnis, R.J. / Brambley, C.A. / Stamey, B. / Green, W.C. / Gragg, K.N. / Cafferty, E.R. / Terwilliger, T.C. / Hammel, M. / Hollis, T.J. / Miller, J.M. / Gainey, M.D. / Wallen, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2022
Title: A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence.
Authors: McGinnis, R.J. / Brambley, C.A. / Stamey, B. / Green, W.C. / Gragg, K.N. / Cafferty, E.R. / Terwilliger, T.C. / Hammel, M. / Hollis, T.J. / Miller, J.M. / Gainey, M.D. / Wallen, J.R.
History
DepositionJun 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: 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_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunity repressor
B: DNA (5'-D(P*TP*TP*TP*CP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*CP*GP*GP*G)-3')
C: DNA (5'-D(P*CP*CP*CP*GP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*GP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,5313
Polymers36,5313
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS and MALS confirm a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-42 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.490, 43.510, 89.280
Angle α, β, γ (deg.)90.000, 102.257, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Immunity repressor


Mass: 23642.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage TipsytheTRex (virus)
Gene: SEA_TIPSYTHETREX_75 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D1GKF7
#2: DNA chain DNA (5'-D(P*TP*TP*TP*CP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*CP*GP*GP*G)-3')


Mass: 6526.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage TipsytheTRex (virus)
#3: DNA chain DNA (5'-D(P*CP*CP*CP*GP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*GP*AP*AP*A)-3')


Mass: 6362.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage TipsytheTRex (virus)

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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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 5-12% PEG 8,000, 0.1-0.3 M CaCl2, and 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11608 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11608 Å / Relative weight: 1
ReflectionResolution: 3.13→47.39 Å / Num. obs: 9005 / % possible obs: 94.43 % / Redundancy: 2 % / Biso Wilson estimate: 92.15 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 12.2
Reflection shellResolution: 3.13→3.24 Å / Num. unique obs: 666 / CC1/2: 0.748 / CC star: 0.925

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMAC1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TZ1

7tz1


Resolution: 3.13→47.39 Å / SU ML: 0.4219 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 850 9.95 %
Rwork0.2087 7692 -
obs0.2125 8542 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.4 Å2
Refinement stepCycle: LAST / Resolution: 3.13→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 861 0 0 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012393
X-RAY DIFFRACTIONf_angle_d1.59853413
X-RAY DIFFRACTIONf_chiral_restr0.0855367
X-RAY DIFFRACTIONf_plane_restr0.0116291
X-RAY DIFFRACTIONf_dihedral_angle_d30.209601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.330.33361240.32761070X-RAY DIFFRACTION79.6
3.33-3.580.34581330.29271228X-RAY DIFFRACTION92.9
3.58-3.940.27961430.22791308X-RAY DIFFRACTION96.99
3.95-4.520.25821470.20241329X-RAY DIFFRACTION98.99
4.52-5.690.2681480.19931353X-RAY DIFFRACTION99.27
5.69-47.390.18991550.1761404X-RAY DIFFRACTION98.92
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)
16.21109969782-1.853679541041.326157706869.585950020611.466352300825.746957643621.08083513488-0.3623215657910.2261522390011.00491508409-1.278098434471.15046167430.988962637580.0336107407912-0.3547267067240.3389767532390.111592446249-0.3277605983570.6208133506130.003043223313821.1822349193848.88448033064.9757008682981.686298393
23.732498944340.2619084090512.897381393271.58914066978-0.3735497655934.237657028910.739153739150.0466284689397-0.506217469702-0.971797610925-0.450087636289-0.527290960350.3918252452610.503595190014-0.3382157180810.5360489118590.226767125506-0.1138652727050.767788431791-0.2333794549560.98629307713247.9348678396.3831964498770.1147366997
35.809153667321.809815821851.169155074095.27249275727-0.7136921282163.979657564210.1534655623260.226626494591-0.100025496311-0.1403797817920.1253028627331.229385571610.21970301814-0.725534346343-0.1568545828190.7198185792750.191596523535-0.1152531456181.00422568177-0.08310663252740.85276819574728.213162666111.900455743461.7046290889
46.62153399404-1.4563645955-0.3006458191014.2241221272.220428645054.90718987620.3455270829211.39035110627-0.796894109073-1.15361448426-0.08838636390730.07364578766570.255581743833-0.565199147696-0.1437022910841.120688190320.122821023199-0.3077899485910.991573900135-0.03668427897580.68398561867228.02209925512.145718679850.6753263438
59.48525503592-0.01226045910241.775274563527.060650077640.4599487447673.54567115819-0.984865640953-2.14101378073-0.004171851334580.8658143881450.2472069816031.910640960140.1252128962860.07932024417780.02581583592720.8819457174920.536719810590.1193917078661.457599583960.1232609699651.7519143762716.645759831322.617585058869.429680954
65.24357641558-1.345118301591.495325974992.70416798296-0.9009421753210.462848637489-1.26055989140.00787621370014-0.2597930256030.8728179837320.8168773693-1.18029884602-1.56165355361-0.8260693865380.3749053108330.8961308057980.202017231433-0.0989413435451.056999523320.03022233305891.2953374535334.902179868525.513370314470.4270249058
77.12438796932-0.5739856118341.638195340325.28743855683-0.6498429455523.546153644530.336495289261.686044353451.63530113928-0.532294684020.236289539174-1.132490364040.5351177807581.566728934420.1237279606160.6215069463070.251889270656-0.04429165368141.339651583090.02119318901911.1251526523849.295305167113.718012875767.9207325964
86.26457502999-1.810095289034.181745989913.06205293725-2.208805853796.23742756777-0.7274002034130.514598297622-0.6898299028540.5290582157320.682010271763-0.943771091028-1.805443163670.8201850781660.4659008718340.8381492446010.1328383199510.06949235634331.59894718187-0.0648432509341.6022687181867.326457869914.875213423770.2665017621
94.79674402877-1.44782388179-1.998613801544.98565680036-1.203771376059.04203789368-0.5265240053032.17464412843-2.519755744-0.4323792093741.51533819557-2.087862142261.262580510291.111981644370.2295895091740.9539450671960.3098462889170.277689549891.680769427680.01263404538182.5104227639973.80266011256.4392136422377.4827258819
106.33552425113-1.748175874023.472335684348.28704753812-4.013054730113.1242031716-0.8224621689872.478876902390.277757556566-2.141931228710.346161490557-0.8535835598320.9599409174751.22578113734-0.4234872911420.7907827610280.3001978991140.2516845275161.83727142497-0.2507210119251.7943619977366.23214682066.2038547015871.0267818933
116.08732541683-0.1780883298925.392549058441.365176238390.2636159398254.80225248604-1.546657063071.50116723546-0.575299382512-0.296974992604-0.102053172757-0.486225505471-1.210068962051.457218805390.5788683534320.6692288163370.125795514833-0.01292384638090.9893300896380.06328579934761.2479268171355.158790310820.802654831168.9870548572
126.38185213108-2.038868513113.861902970265.26730322855-0.359014306562.6677212426-0.348337232355-1.622711514760.8777988027180.863277466174-0.02772301393590.1220409162790.06444505637221.31088845239-0.03000057779040.6669579462540.238064643615-0.1075369347711.20492942833-0.1026694432671.0408574648636.839968805617.039034510367.7102768001
137.78347914039-1.818014664153.144662373661.85302008063-0.841404802881.20785177838-0.282277285771-0.4318043193550.3024557668160.9208526481930.9366680546332.30230143822-0.766741294572-0.3302347698040.1601763769131.084193742550.479754824401-0.02700548087481.37231312819-0.05507596725121.8316268121121.871716550728.650545553171.9970102374
142.003028005728.88484192497.948961575597.500726971966.71460861186.12304091837-1.49885949782.003163120380.833890204170.1793823547030.1780602160791.71042016741-0.683639747832-0.382459509283-0.2215576700230.9824889820220.7154122205080.4652556970082.116947979210.2787235236951.7639706661811.803006063328.70907452464.9271886974
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 40 )AA15 - 401 - 26
22chain 'A' and (resid 41 through 68 )AA41 - 6827 - 54
33chain 'A' and (resid 69 through 118 )AA69 - 11855 - 104
44chain 'A' and (resid 119 through 181 )AA119 - 181105 - 167
55chain 'B' and (resid 22 through 26 )BB22 - 26
66chain 'B' and (resid 27 through 31 )BB27 - 31
77chain 'B' and (resid 32 through 36 )BB32 - 36
88chain 'B' and (resid 37 through 41 )BB37 - 41
99chain 'B' and (resid 42 through 42 )BB42
1010chain 'C' and (resid 60 through 64 )CC60 - 64
1111chain 'C' and (resid 65 through 69 )CC65 - 69
1212chain 'C' and (resid 70 through 74 )CC70 - 74
1313chain 'C' and (resid 75 through 79 )CC75 - 79
1414chain 'C' and (resid 80 through 80 )CC80

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