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- PDB-7vjq: Pectobacterium phage ZF40 apo-aca2 complexed with 26bp DNA substrate -

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Basic information

Entry
Database: PDB / ID: 7vjq
TitlePectobacterium phage ZF40 apo-aca2 complexed with 26bp DNA substrate
Components
  • (DNA (27-MER)) x 2
  • anti-CRISPR-associated protein Aca2
KeywordsTRANSCRIPTION/DNA / anti-crispr / Aca2 / anti-crispr-associated protein / crispr / repression / complex / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homologyProtein of unknown function DUF1870 / Domain of unknown function (DUF1870) / YdiL domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / metal ion binding / DNA / DNA (> 10) / DUF1870 family protein
Function and homology information
Biological speciesPectobacterium phage ZF40 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 20, 2021ID: 7CQA
Revision 1.0Oct 20, 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
A: anti-CRISPR-associated protein Aca2
B: anti-CRISPR-associated protein Aca2
C: DNA (27-MER)
D: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,79612
Polymers44,0964
Non-polymers7008
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-94 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.310, 168.473, 41.492
Angle α, β, γ (deg.)90.000, 90.060, 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
Components on special symmetry positions
IDModelComponents
11B-203-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein anti-CRISPR-associated protein Aca2


Mass: 13752.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium phage ZF40 (virus) / Gene: ZF40_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: H9C180

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (27-MER)


Mass: 8297.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8293.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 44 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.12 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.1M Tris pH 8.0, 1.6M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.79→40 Å / Num. obs: 21080 / % possible obs: 95.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.18 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.91
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1712 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000v705cdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CQ9

7cq9
PDB Unreleased entry


Resolution: 2.79→38.48 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.1706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 841 4.79 %
Rwork0.1901 16716 -
obs0.1916 17557 79.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.35 Å2
Refinement stepCycle: LAST / Resolution: 2.79→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 1101 38 36 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293229
X-RAY DIFFRACTIONf_angle_d0.54824598
X-RAY DIFFRACTIONf_chiral_restr0.0326501
X-RAY DIFFRACTIONf_plane_restr0.0031400
X-RAY DIFFRACTIONf_dihedral_angle_d27.9672806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.970.34760.26521759X-RAY DIFFRACTION50.21
2.97-3.20.2951790.24712170X-RAY DIFFRACTION61.31
3.2-3.520.2341250.21012609X-RAY DIFFRACTION75.07
3.52-4.020.23221940.17953260X-RAY DIFFRACTION94.42
4.03-5.070.20592010.16783439X-RAY DIFFRACTION98.89
5.07-38.480.18491660.18113479X-RAY DIFFRACTION97.98
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)
14.060852957881.4293824094-0.3610487332518.579075398294.318659306363.32855569062-0.009012045413580.210492540490.398219167126-0.542862990666-0.01582202998030.279053335751-0.5634808406040.11796829721-0.2518380932550.202920524573-0.1589037434760.02388921179720.1165395315710.01380301422490.19911580465316.715255213514.2457442335-2.55319798443
21.738933432710.77521224389-0.3596915905771.77165581681-0.3392390433020.764234903428-0.06279236681640.1671308466150.1282910123170.009493770845770.00185951254616-0.103970114546-0.2242766540050.09113579022560.05085584393280.323258170996-0.242499792631-0.0695786038661-0.002660556297590.005003954488470.19244667319616.35721971736.91672281023-9.10261013901
32.910709490421.74416188282-2.932179865186.03687124209-5.11287128197.37197506801-0.2816785191540.0688381749827-0.3846161779580.2492641805770.00842408744631-0.2661872959641.093663171790.2777099711140.3090655111990.3094469166670.0723662055012-0.0007891014865270.10608103665-0.03228226436360.16882459043418.8806254677-10.2033658005-12.5522902593
40.4849081540320.0726809907648-0.4110000115640.659042727266-0.1862379921161.249879791270.0151503480056-0.0124190819869-0.1689137083460.226560133025-0.0706779526910.0718189638922-0.161863547247-0.06601716408120.009126068932660.2567931085560.0335683422825-0.01792631182970.05239710175410.02700719505210.23756460774813.5697261567-5.67612703761-7.94691722266
54.30805005394-1.981291052976.262290737020.939347822892-2.882219374249.1032928599-0.318995105683-0.61666303188-1.44891072880.299058337163-0.7511467496970.8406642858973.07193477786-1.94245457291.192240440280.823127112292-0.1467190334690.1358210786150.464159780548-0.08633510083440.56102841391913.1855001302-18.84361455285.71613254532
60.876995617923-0.5453958561860.4784175721651.2474691731-0.1355066187080.566962902362-0.144645310634-0.0578853688497-0.001477283835620.0616312277141-0.00665222793727-0.3579878910930.2592694299830.195686941151-0.2123004748250.3701259710510.252193518190.1138952149630.07597455139130.02185722893150.32763293308823.9663077185-9.96051100536.17139809855
74.88430718984-3.095095564680.8313132926922.56985826754-0.3766288418471.01318080489-0.304360533896-0.424512453615-0.3061665127690.6959334596860.3859378069750.1450448659150.279315652166-0.0736310664139-0.02949329618210.3234033469030.05434269300050.05034911547050.1361158150010.01756654919240.1203018307118.16150274069-2.4156058416210.9121042979
83.10585865470.918227990512.552242598892.2012437987-2.196440202626.60984530562-0.136796041978-0.485015252470.7532507424390.3973205607960.153199880274-0.135149160746-0.801417226755-0.8585660118680.1903342672370.602009989090.20270587994-0.06643584028770.287379526278-0.0658554566950.4830855580580.40808231734416.248145386.99142390296
98.31729774201-7.361730924274.624387466518.92531599881-3.068858947278.14872065901-0.923928786737-0.1551540150821.130523885180.4859609827170.343716175485-0.625168284293-0.781672156383-0.07390947118260.3272177457250.546056035134-0.0255372338837-0.088041620260.1754357402950.01703800074330.26678510355316.596764047713.62680023059.1794510953
101.35084728559-1.669967006813.170549041035.32668564016-1.408006333129.373547767070.6356062561420.2781881810320.827421897311-0.0158220833649-0.317141502599-0.767479901232-1.113156837050.653580042620.2850446308980.245939548002-0.00841048405220.1323725672810.1335905269050.019808608650.25906187343522.20456873110.339270791815.9929349082
111.295107122750.2884047143480.7079129085321.10731180476-0.5673217123821.725723513330.0375998631863-0.01557723552110.243453200461-0.129700010505-0.1034084300070.03489962673090.1325407367560.006490948786390.06613620950220.260967874211-0.04684782100920.002457776839790.06183308839110.004175288384010.19438624198213.69078083337.834721894498.24366116534
120.899805271596-0.7147743668020.5242665053350.7160424019290.06078206599561.82234256181-0.1433026518650.138841677395-1.75668358312-1.00828604199-0.272439842241-0.8678288592921.735373606090.852909066825-0.7063297736611.118881092550.1837481676290.2240105889460.4868199075130.130205842291.2318218104434.4049817638-25.85146195489.33610589355
136.31703751505-0.3009968852250.6868725797650.0147168429373-0.1318876504122.729474767270.013837730460.5843202298270.5880617146040.0479569424861-0.977484849370.0126878097506-0.5708735730091.204895933230.4001175951910.531084668615-0.205911945717-0.1868972458620.8608991442720.2465813656070.91122068804338.076103636514.1841912237-5.7766340012
144.430912686793.10930122992-2.309741328492.75651696093-2.604840327112.885109938220.428742345889-0.1448876973691.68409163323-0.153113124802-0.00564041014325-1.87156100094-1.557753731470.332047785053-1.111586791092.650655358550.126953791699-0.5017047544360.746912757413-0.08964899671752.4255746041433.487610254537.0716170134-8.64858883792
152.632952749941.91349723396-0.704833291491.57793139092-1.307923046323.486528079280.2244851519270.162105279150.04120674439070.572358908091-0.980385805557-1.06660290538-0.3594488750021.672874859290.7066055801040.46650717318-0.110452239879-0.1107080184380.6919368992450.2110461189040.80881698340839.018643354913.1238180658-4.118330173
163.371137259920.436193516695-1.499612441210.2196323290450.2383908342631.821218513130.262559943471-1.15771392444-0.825210730027-0.291355586763-0.2160074232730.1840850920050.5625640049560.8834335558970.1811284380370.6233157088070.3558177171380.1821596967480.7914074661080.2577451171940.98680490386237.8461510659-17.7838893845.87144256484
175.87585964793.685646880012.847050187183.444238201372.33296411671.64382348458-0.3478344715970.155674250435-1.278560104550.151440392168-0.478742328312-0.9376146425790.4121362380250.305729173290.9377418501471.270062687830.2957491375740.4828223065511.215299452970.4296198063582.2599406936728.3986700773-33.517617117515.3400207733
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -3 through 12 )AA-3 - 121 - 16
22chain 'A' and (resid 13 through 74 )AA13 - 7417 - 78
33chain 'A' and (resid 75 through 88 )AA75 - 8879 - 92
44chain 'A' and (resid 89 through 116 )AA89 - 11693 - 120
55chain 'B' and (resid -3 through 2 )BB-3 - 21 - 6
66chain 'B' and (resid 3 through 43 )BB3 - 437 - 47
77chain 'B' and (resid 44 through 69 )BB44 - 6948 - 73
88chain 'B' and (resid 70 through 74 )BB70 - 7474 - 78
99chain 'B' and (resid 75 through 81 )BB75 - 8179 - 85
1010chain 'B' and (resid 82 through 87 )BB82 - 8786 - 91
1111chain 'B' and (resid 88 through 116 )BB88 - 11692 - 120
1212chain 'C' and (resid 1 through 10 )CC1 - 10
1313chain 'C' and (resid 11 through 27 )CC11 - 27
1414chain 'D' and (resid 1 through 5 )DD1 - 5
1515chain 'D' and (resid 6 through 15 )DD6 - 15
1616chain 'D' and (resid 16 through 25 )DD16 - 25
1717chain 'D' and (resid 26 through 27 )DD26 - 27

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