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- PDB-7vjm: Aca1 in complex with 19bp palindromic DNA substrate -

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Basic information

Entry
Database: PDB / ID: 7vjm
TitleAca1 in complex with 19bp palindromic DNA substrate
Components
  • DNA (5'-D(*AP*TP*TP*AP*GP*GP*CP*AP*CP*AP*TP*TP*GP*TP*GP*CP*CP*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*GP*GP*CP*AP*CP*AP*AP*TP*GP*TP*GP*CP*CP*TP*AP*A)-3')
  • anti-CRISPR-associated protein Aca1
KeywordsTRANSCRIPTION/DNA / CRISPR / anti-CRISPR / anti-CRISPR-associated / DNA binding / autoregulation / TRANSCRIPTION / Aca1 / complex / TRANSCRIPTION-DNA complex
Function / homologylambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / DNA / DNA (> 10) / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLiu, Y.H. / Zhang, L.S. / Wu, B.X. / Huang, H.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2.
Authors: Liu, Y. / Zhang, L. / Guo, M. / Chen, L. / Wu, B. / Huang, H.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 13, 2021ID: 7C0H
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: 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 / _citation.year
Revision 1.2Nov 29, 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
B: anti-CRISPR-associated protein Aca1
A: anti-CRISPR-associated protein Aca1
D: DNA (5'-D(*AP*TP*TP*AP*GP*GP*CP*AP*CP*AP*TP*TP*GP*TP*GP*CP*CP*TP*AP*T)-3')
C: DNA (5'-D(*TP*AP*TP*AP*GP*GP*CP*AP*CP*AP*AP*TP*GP*TP*GP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,9054
Polymers30,9054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-56 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.710, 42.710, 362.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#1: Protein anti-CRISPR-associated protein Aca1


Mass: 9319.603 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD30 (virus) / Gene: JBD30_036 / Production host: Escherichia coli (E. coli) / References: UniProt: L7P845
#2: DNA chain DNA (5'-D(*AP*TP*TP*AP*GP*GP*CP*AP*CP*AP*TP*TP*GP*TP*GP*CP*CP*TP*AP*T)-3')


Mass: 6123.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*TP*AP*GP*GP*CP*AP*CP*AP*AP*TP*GP*TP*GP*CP*CP*TP*AP*A)-3')


Mass: 6142.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M di-Ammonium tartrate; 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 6553 / % possible obs: 87 % / Redundancy: 11.3 % / Biso Wilson estimate: 62.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.1
Reflection shellResolution: 3→3.16 Å / Num. unique obs: 878 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FA3

7fa3


Resolution: 3→29.79 Å / SU ML: 0.3809 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.2855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 340 5.26 %
Rwork0.1949 6130 -
obs0.1981 6470 85.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.4 Å2
Refinement stepCycle: LAST / Resolution: 3→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 797 0 0 1948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412069
X-RAY DIFFRACTIONf_angle_d0.6882968
X-RAY DIFFRACTIONf_chiral_restr0.0345323
X-RAY DIFFRACTIONf_plane_restr0.0071252
X-RAY DIFFRACTIONf_dihedral_angle_d32.9054551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.780.33031460.2312764X-RAY DIFFRACTION80.08
3.78-29.790.22631940.18033366X-RAY DIFFRACTION90.96
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)
10.00850733590576-0.0143993359041-0.03048698518570.07235140652890.07298935380760.0951709517054-0.216148580814-0.155000045476-0.04268193053050.0802766219321-0.001899497260090.1623556831270.825127367461-0.00374882749119-0.0107827894380.3512882375530.08230988236640.1019835955160.4775000688210.1966541141980.5535765859038.00098312203-19.9311489627-15.4029943334
20.05097398039950.04761411147850.005832806965680.0802324589292-0.03615474009580.0592660759198-0.229113851408-0.4851372825380.2870881559280.1961099423490.359659381728-0.0535379074447-0.2039470779920.182881288724-0.001304716311170.2787498748010.05069431260240.09117364021030.658665222030.011420840320.3187146511338.67670421758-6.29901537718-11.2428832308
30.004970389088190.01299215518560.00202778779670.0373860469471-0.004170035665260.0217522230467-0.188291168573-0.133900959032-0.127002602378-0.0265644918467-0.2992805092440.6935206903810.0570506372813-0.195444144564-0.000717687066320.325035774103-0.0630917047079-0.03458976540940.53717210467-0.05831159996460.543063347063-1.86164196502-9.88082527538-20.0447757221
40.000222273930897-0.00493280171626-0.00131210891929-0.00493749891512-0.0004778539088990.0031312408121-0.0700565534768-0.287451748123-0.2948321168110.292367226060.002034247016380.01984423832020.0366884259850.134641655703-0.05070420621330.1287339421680.6132270441830.2536116420860.5595038998640.06719493436740.30320458874314.894882403-17.4605186686-12.2812857546
50.0381884734450.0500450469498-0.05625266986870.223707840848-0.2528898192860.5827838706370.0310648350492-0.4346914683830.1133274278510.04348168612260.253002464846-0.134437937140.004065220175520.1816769567280.1811906024260.211172292559-0.01843903873990.05608502918791.08478432524-0.1485763880450.49103117747724.5938184493-8.77240133346-14.4150598513
60.03099093427260.0182788991815-0.07889923197410.0331554688622-0.0336770473920.4279907757090.0214897969228-0.3190880847130.22847771009-0.04022625966660.226928920945-0.4295897437940.004602372243610.7998656260580.435883643721-0.05972037741360.3472887417890.310348013750.845574498075-0.212414762910.2011478605823.8203787333-13.0060107704-30.1078043023
70.469668936879-0.0974120699186-0.168357676260.240960794649-0.120839418740.1772583899690.003757917614410.003081943587460.315624349499-0.1864255323760.142995280687-0.236378469222-0.09346438341910.1048893904490.08486599842870.151017777924-0.399354973097-0.008158777480030.510658839164-0.2798175694280.27163242649823.63790858890.0518625563734-30.9334961723
80.2980023881910.277270593733-0.3920763321080.284888242167-0.3123840454980.543102718310.0754228992655-0.0144871581248-0.676371697852-0.0677922446198-0.0978634098245-0.4275507608290.3918585394240.2048739792230.004737097492690.3530974104060.2518410496380.01222084636670.856058383424-0.01383299015950.4255281902424.0423936756-17.0310521798-20.2853032137
91.15011252414-0.07494447498570.1531909411060.535770925871-0.2517635007090.1321141518860.1128689787-0.3205067173020.319901672670.293020132202-0.1121349642430.256116397556-0.1590833951770.156083039001-0.03800719024110.3271480137470.1054494063880.1030514316650.898420358204-0.002739492199210.4216131246170.609169410474-3.29156025023-5.18323101204
100.01224504619380.01356077190010.003553811266610.0559581743739-0.02423190426870.006745225849870.144224957892-0.1753321954240.658660008241-0.3771102603780.0270641538148-0.26062427967-0.146751028181-0.2168659122390.0002981477550660.6938961251250.321096421150.03741925806280.8874207491770.1129696146160.661903707438-0.0930063514056.01950717565-21.7818239135
110.0108601188866-0.0169275359101-0.006182132309980.0435987432243-0.008846810029460.02570818726020.3470597344730.2356265408740.427537783293-0.48989870917-0.072414977597-0.105525753795-0.1359769964470.005060603994870.001398761112590.420386791919-0.0405450562860.09003064266320.357246097138-0.08720864380560.57046443611211.4890682333-3.38523365685-32.4254081234
120.02720503637140.0106374592966-0.002798762270740.004534555881210.0117700224306-0.002332545770340.2502236431410.0330954106218-0.120812707609-0.44118790358-0.0408911502787-0.2881858335780.160657643657-0.1697119760790.0002554564272880.7647631794950.1590376662740.03890836426940.718933065141-0.04932021764550.37354461061219.0726944953-8.92981277938-48.1084784604
130.01882193589810.0205197982293-0.01776040941110.01031033226460.007559561286380.03040331404090.205946949646-0.0273059118668-0.0856090905264-0.3039419538320.1502502785210.136777509653-0.1843156090970.007249876126510.0008224695790350.5188413018890.09646220988090.118092515720.61330576061-0.08208776442330.47565036340124.591934894-12.7057622457-41.0553993949
140.7860175123270.2344058926020.08926784301110.191332712731-0.3125420104680.962765072020.569587263298-0.1229837403730.497272465201-0.603661517770.1645446334620.0140852733498-0.258200090763-0.5462044438560.348580491520.4801929783970.08216218394350.07583647680830.3967070700990.09824297449690.4344225320018.299689038740.0386858471141-31.3698175779
150.3011115364430.140262687066-0.1782299894790.465623734989-0.5735323046630.7119388946990.27068204703-0.2163907411840.0621084648059-0.1178941681890.5636151451170.266105857495-0.337516719193-0.0336385633080.04463607248220.7986546462320.1112444192930.2426759349530.662028039093-0.109208422490.741452724475-1.915332932036.72976563207-8.65132066788
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 7 through 28 )BA7 - 281 - 22
22chain 'B' and (resid 29 through 50 )BA29 - 5023 - 44
33chain 'B' and (resid 51 through 62 )BA51 - 6245 - 56
44chain 'B' and (resid 63 through 78 )BA63 - 7857 - 72
55chain 'A' and (resid 6 through 17 )AB6 - 171 - 12
66chain 'A' and (resid 18 through 50 )AB18 - 5013 - 45
77chain 'A' and (resid 51 through 62 )AB51 - 6246 - 57
88chain 'A' and (resid 63 through 78 )AB63 - 7858 - 73
99chain 'D' and (resid 20 through 24 )DC20 - 24
1010chain 'D' and (resid 25 through 29 )DC25 - 29
1111chain 'D' and (resid 30 through 34 )DC30 - 34
1212chain 'D' and (resid 35 through 39 )DC35 - 39
1313chain 'C' and (resid 0 through 4 )CD0 - 4
1414chain 'C' and (resid 5 through 14 )CD5 - 14
1515chain 'C' and (resid 15 through 19 )CD15 - 19

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