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- PDB-6wan: Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain conta... -

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Basic information

Entry
Database: PDB / ID: 6wan
TitleStructure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 3'3'3'-cAAA
Components
  • Cyclic RNA (R(P*AP*AP*A)
  • SAVED domain-containing protein
KeywordsHYDROLASE / nuclease / DUF4297 / SAVED / CARF / phage immunity
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
CD-NTase associated protein 4, DNA endonuclease domain / Cap4, dsDNA endonuclease domain / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain
Similarity search - Domain/homology
RNA / CD-NTase-associated protein 4
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Antine, S.P. / Cabrera, V. / Schwede, F. / Mekalanos, J.J. / Shao, S. / Lee, A.S.Y. / Kranzusch, P.J.
CitationJournal: Cell / Year: 2020
Title: CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection.
Authors: Lowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Mathews, I.T. / Antine, S.P. / Cabrera, V.J. / Kashin, D. / Niemann, P. / Jain, M. / Schwede, F. / Mekalanos, J.J. / Shao, S. ...Authors: Lowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Mathews, I.T. / Antine, S.P. / Cabrera, V.J. / Kashin, D. / Niemann, P. / Jain, M. / Schwede, F. / Mekalanos, J.J. / Shao, S. / Lee, A.S.Y. / Kranzusch, P.J.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: 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.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAVED domain-containing protein
B: SAVED domain-containing protein
C: SAVED domain-containing protein
D: SAVED domain-containing protein
E: SAVED domain-containing protein
F: SAVED domain-containing protein
G: Cyclic RNA (R(P*AP*AP*A)
H: Cyclic RNA (R(P*AP*AP*A)
I: Cyclic RNA (R(P*AP*AP*A)
J: Cyclic RNA (R(P*AP*AP*A)
K: Cyclic RNA (R(P*AP*AP*A)
L: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,49018
Polymers318,91412
Non-polymers5766
Water8,863492
1
A: SAVED domain-containing protein
G: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAVED domain-containing protein
H: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAVED domain-containing protein
I: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SAVED domain-containing protein
J: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: SAVED domain-containing protein
K: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: SAVED domain-containing protein
L: Cyclic RNA (R(P*AP*AP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.498, 111.184, 163.748
Angle α, β, γ (deg.)90.000, 100.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
SAVED domain-containing protein / Cap4


Mass: 52209.676 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: HMPREF0023_0548 / Production host: Escherichia coli (E. coli) / References: UniProt: C0VHC9
#2: RNA chain
Cyclic RNA (R(P*AP*AP*A) / 3'3'3'-cAAA


Mass: 942.660 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 0.2 M LiSO4, 16% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→38.8 Å / Num. obs: 145531 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 50.81 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 13668 / CC1/2: 0.428

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VM6

6vm6


Resolution: 2.4→38.8 Å / SU ML: 0.288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0235
RfactorNum. reflection% reflection
Rfree0.2396 2000 1.38 %
Rwork0.2078 --
obs0.2082 145186 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20894 0 426 492 21812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002321808
X-RAY DIFFRACTIONf_angle_d0.604829575
X-RAY DIFFRACTIONf_chiral_restr0.04223278
X-RAY DIFFRACTIONf_plane_restr0.00333719
X-RAY DIFFRACTIONf_dihedral_angle_d16.77727846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.33281310.30489384X-RAY DIFFRACTION91.11
2.46-2.530.36411430.290310246X-RAY DIFFRACTION99.21
2.53-2.60.31761440.287210255X-RAY DIFFRACTION99.58
2.6-2.680.36051420.265210226X-RAY DIFFRACTION99.64
2.68-2.780.3241440.254510305X-RAY DIFFRACTION99.8
2.78-2.890.28471430.243910252X-RAY DIFFRACTION99.59
2.89-3.020.24341430.235810230X-RAY DIFFRACTION99.24
3.02-3.180.25221420.236610127X-RAY DIFFRACTION98.13
3.18-3.380.25991440.226610298X-RAY DIFFRACTION99.99
3.38-3.640.24921450.217510354X-RAY DIFFRACTION99.95
3.64-4.010.24431430.194610291X-RAY DIFFRACTION99.63
4.01-4.590.19841440.173210326X-RAY DIFFRACTION99.37
4.59-5.780.2091450.18210374X-RAY DIFFRACTION99.82
5.78-38.80.19181470.173810518X-RAY DIFFRACTION99.34
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)
10.1692603785610.14659365163-0.1667496150070.2597983084030.1045852553990.1718844368080.008741608479570.0483941019057-0.01838166062370.008006197251820.02492531627060.03451276447560.0378902117703-0.0854853333875-1.79727181199E-100.307984708615-0.01391847240260.02682367283850.3991011942530.008742688241290.334853530407-12.506090404218.699810649949.8807173042
20.147697767099-0.189688932349-0.1118357341350.0864316231633-0.1013316073760.2788481248840.05084024879770.0419497761904-0.01434067386450.0803186313905-0.07823928778070.09703985444230.03398757611330.03059367185643.97072158042E-90.426471696721-0.0843694220580.02514828566660.3343139825790.01714303097610.363898273961-3.368392368126.89967077876.2675085272
30.1283403818920.1341556651540.07484694394240.194121921825-0.05464480326780.185321637013-0.152707228197-0.05987311502270.07148032489620.4484193068550.120683952028-0.131500004934-0.1220624657270.172473292506-1.88230982461E-90.627970971256-0.131106730086-0.07341322624160.493603832842-0.01643938890560.36491719876610.210626742524.318817314295.0050245108
40.168864192090.06145192469660.2073031108540.319703882384-0.08204965867880.139593505493-0.01741407607180.09183987456050.0277152140557-0.01599617878670.0589453690544-0.110755445205-0.0189038694348-0.01179588428678.36008378579E-100.308858480985-0.00788562026150.0479189281480.389430778857-0.06289931643090.39255197766836.17033546120.755289201621.0677650734
50.136079224237-0.04616296822530.130561595114-0.07247440725310.04442457288880.04910747231920.03380791188310.0102537567252-0.0146450699836-0.12012347538-0.03359909444160.0504942457795-0.02870595419030.05601667350715.44459671087E-90.3018085593330.00375347963456-0.01444784464830.344808649376-0.02825146284630.48077142016651.323377722714.195552368341.1577952726
60.1452268164710.126204341785-0.01259834399590.284932854277-0.1063255741030.0701134979120.119866162708-0.0283625241816-0.08215101257070.1192577644070.0257776389402-0.4436475997110.108884356355-0.008854870939866.03783802737E-90.44361866652-0.00654193516923-0.05833124463720.6050650058520.04143111195260.6870578747768.881811248216.111703594559.8670366741
70.08895295938160.001343783498430.1236128739170.0283218153068-0.07345270910080.1686425873220.0618239370339-0.0579883748288-0.07789666527940.316972577047-0.0134342569135-0.2884695047040.0748711406659-0.08188216629984.95639546115E-80.313561942632-0.0105965181251-0.05923121523630.3913029417440.03707855794220.53956842769762.322510991214.961453063759.9653459531
80.1101010177190.117727536539-0.07536338136990.038687069986-0.04952963408350.1210533720920.04097485742380.01337534193180.06799290701690.02321444250610.00449196693232-0.02905645203040.0398292055782-0.03720074329615.94143400009E-90.3585186599090.05346635415790.01303164023850.3729617705770.007301373792740.327552633345.7876162190541.323822559629.9010589083
9-0.01589306486270.01765871922220.06807471602740.140057587076-0.05907317945210.0172691769542-0.08921463973580.141028588620.147575488741-0.05115695885460.13849420943-0.0653511569473-0.0907956949130.0386783484911-5.55960686979E-80.4062397977430.000695720063228-0.005500198383570.3568647744960.04829733988050.3776053541928.3702328576848.989063475825.3031325529
100.226493510596-0.279559317881-0.01487215399010.249050136515-0.2128269171750.2988050138490.0890437760980.042306058781-0.0168986163614-0.0669249216062-0.0402203283991-0.009826402398570.0505558972292-0.04622717539034.69993887273E-100.376289815453-0.004519567771450.01209545330730.4014986141550.008993408717450.2726209360422.5882876304530.12477170835.13806211456
110.0657763546561-0.0158751842211-0.05366773534180.1395490828890.04134874006310.08513089278420.1741244583430.734680785094-0.3696839165-0.0627599592521-0.233793078624-0.1855653563220.0558854970461-0.214343404349-4.28794218524E-90.6344128165520.09267084098540.06221364573650.865368445607-0.2458031416010.41048652771316.857791266216.9885995518-13.8957764745
120.148768741965-0.0762722533088-0.04069893655960.0854869559920.111203846177-0.0202901799611-0.0292791960722-0.07717984076570.008139168264070.0317164180215-0.000780984081414-0.05711479043330.0109399224654-0.0772908309495-2.73829787491E-90.4231698094580.0313391812371-0.04062659016710.2904533885370.01096891241410.33177309693619.69299211374.774926713760.9349755081
130.149099130586-0.140816659085-0.1976635152910.152710621462-0.09379090106810.105545258210.000982667114735-0.00198837843254-0.001160697405810.127703649095-0.0307865362624-0.03709480789340.0901376036448-0.126202586269-7.11447678301E-90.466573215209-0.0128385456943-0.07203553903790.2903955203760.03279611483260.37103055907923.6614352042-0.41356786943165.7884146273
140.18119306545-0.04438796565050.00554762263156-0.0161518728490.08958232800090.1284026660890.02485097911510.0423539734175-0.08724065243550.0706000375291-0.0224319310541-0.0564986358990.005888829913580.00825815476956-1.41018770615E-90.4432114368070.0224906974512-0.03189962967050.340134542014-0.03220353739310.47880022315337.6330823209-10.767596045646.0993888999
15-0.0521651766183-0.127970392504-0.0541923921260.05198025430530.004626738547330.08004528274540.06469065136030.70401769977-0.412507473486-0.2280291085381.09706275098-0.2132442730840.463222874178-0.0721084866853-4.11116177277E-90.4011290378290.8257522408130.30930162565-0.808897013202-1.545045086310.67214610820144.9714861658-24.239692833827.4153007191
160.04531502709740.0102322812233-0.0905921345550.0395841256955-0.01242753266120.06696372787310.05195767851170.07387517085550.05294636866270.002733573647090.023574756171-0.05757483319530.0385136878112-0.03883853982424.06134534416E-80.3454156893130.022219231587-0.06069732135430.296697232322-0.05075037107970.39853104158228.256998242433.681845402155.9969298157
170.005993114232720.02811018907210.001255775516320.002216239263460.005482470009730.04368311939560.02147483045010.00255665430285-0.02726486401140.01618027860120.0416744638841-0.111743951005-0.136558384556-0.0131163236165-2.41275665494E-80.380437393009-0.0201370525516-0.01056610157570.362456886635-0.0597213696060.45153139768135.034745592941.030542143249.027641665
180.16338742819-0.0172706013269-0.0652190727750.1753748186710.07020247541620.04542621643190.06658128709290.0699550608386-0.004908192966490.0507780150546-0.00849075082975-0.1832758348-0.06214716125930.06162134094273.05367299285E-90.359979195502-0.00998504001587-0.06782923587820.28599169592-0.01833879083990.4113151649132.369296180841.047838436559.7496767589
190.0755440824694-0.1537296618440.1184718728780.2752327304-0.1243528669860.1560005026070.04154933190190.0349970335806-0.0584150287870.08665647116040.0376371514367-0.0447082769757-0.108282445466-0.09747552215091.02935765096E-80.3560384505230.03394029630720.01298611805920.288536756409-0.002248589184180.3280088330526.6348280578752.100668783863.4597620644
200.1630326997570.00561346743281-0.002883484500240.124957337877-0.002394586166620.00724429136016-0.2701526920260.0251287898782-0.1242142550040.09997512068730.5544284225050.0873432588989-0.36956526057-0.571131399584-8.65752778227E-100.4330734392540.3167544697550.1538296065650.53770236920.1445737396140.397502860496-13.023510365863.244324873157.7058167865
210.158987115553-0.0638414060712-3.79597788195E-50.173365762421-0.009819306892670.1885347847440.02688515235050.0930517505691-0.04501372898030.0699839085091-0.004107360628290.02139578720040.0909697346584-0.0194316753494-4.16653052957E-90.406999738008-0.0212506751913-0.03205226314770.355901907054-0.08156039595420.3642326749299.16471449891-4.4671190938830.8217023024
220.00250765810936-0.00697314214240.0360025315330.01082961798280.0005824865896050.0126025551191-0.1754293792240.06255634732150.01874178735060.02871922860560.07242884689250.02089970682260.0528954197516-0.1480525882974.19619033107E-80.396994384929-0.0535020868268-0.007582806280780.426465916003-0.09424052610390.3705587676029.28046195729-3.251927172146.05979767189
230.2558418168890.0728014859791-0.12822243931-0.00830209718208-0.0692588425280.2960132433110.02391903376280.09913451763880.146423872563-0.02880846940870.0254225019857-0.08867477262160.147138381082-0.160903707191-2.3284666436E-90.322739381571-0.0612211256753-0.005392668728280.481606351572-0.02925409431390.317633564992-14.977440538810.352676985114.6361706638
240.03183548050920.03695118189560.01179510835610.0597558742098-0.0486020391340.01189404264610.007034338152440.01019022857990.2058955308320.3426974209860.1316658183140.133268180871-0.118760079803-0.223494564701-9.13858022642E-70.548163548230.00109776490225-0.02444565806991.90123429470.1829554823450.825069285144-40.308808140719.222047755917.6590684129
250.0327462927895-0.06409064566050.0188190389330.03504390488580.05946644526040.0241728236340.09216910211470.7601740669430.6326946152770.4881352029350.1587528771170.199908704479-0.00463849196495-0.573030214157-6.03544284398E-80.304397767998-0.00782388624073-0.006668233641061.111530857160.2016398821710.566504701889-30.150854374420.012129119215.441456794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 209 )
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 342 )
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 462 )
4X-RAY DIFFRACTION4chain 'B' and (resid 14 through 209 )
5X-RAY DIFFRACTION5chain 'B' and (resid 210 through 318 )
6X-RAY DIFFRACTION6chain 'B' and (resid 319 through 393 )
7X-RAY DIFFRACTION7chain 'B' and (resid 394 through 462 )
8X-RAY DIFFRACTION8chain 'C' and (resid 14 through 133 )
9X-RAY DIFFRACTION9chain 'C' and (resid 134 through 189 )
10X-RAY DIFFRACTION10chain 'C' and (resid 190 through 342 )
11X-RAY DIFFRACTION11chain 'C' and (resid 343 through 462 )
12X-RAY DIFFRACTION12chain 'D' and (resid 14 through 133 )
13X-RAY DIFFRACTION13chain 'D' and (resid 134 through 209 )
14X-RAY DIFFRACTION14chain 'D' and (resid 210 through 330 )
15X-RAY DIFFRACTION15chain 'D' and (resid 331 through 462 )
16X-RAY DIFFRACTION16chain 'E' and (resid 15 through 91 )
17X-RAY DIFFRACTION17chain 'E' and (resid 92 through 133 )
18X-RAY DIFFRACTION18chain 'E' and (resid 134 through 209 )
19X-RAY DIFFRACTION19chain 'E' and (resid 210 through 342 )
20X-RAY DIFFRACTION20chain 'E' and (resid 343 through 462 )
21X-RAY DIFFRACTION21chain 'F' and (resid 14 through 172 )
22X-RAY DIFFRACTION22chain 'F' and (resid 173 through 209 )
23X-RAY DIFFRACTION23chain 'F' and (resid 210 through 361 )
24X-RAY DIFFRACTION24chain 'F' and (resid 362 through 395 )
25X-RAY DIFFRACTION25chain 'F' and (resid 396 through 461 )

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