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- PDB-6vm6: Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain conta... -

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Basic information

Entry
Database: PDB / ID: 6vm6
TitleStructure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 2'3'3'-cAAA
Components
  • 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
  • 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 sp. ATCC 27244 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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
DepositionJan 27, 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 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
H: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
I: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
J: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
K: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,74019
Polymers317,97111
Non-polymers7698
Water26,8421490
1
A: SAVED domain-containing protein
G: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area21470 Å2
2
B: SAVED domain-containing protein
H: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-12 kcal/mol
Surface area21540 Å2
3
C: SAVED domain-containing protein
I: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3444
Polymers53,1522
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-19 kcal/mol
Surface area21280 Å2
4
D: SAVED domain-containing protein
J: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-11 kcal/mol
Surface area21520 Å2
5
E: SAVED domain-containing protein
K: 2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2483
Polymers53,1522
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-12 kcal/mol
Surface area21200 Å2
6
F: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4023
Polymers52,2101
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-18 kcal/mol
Surface area21820 Å2
Unit cell
Length a, b, c (Å)106.577, 111.457, 164.830
Angle α, β, γ (deg.)90.000, 100.207, 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 sp. ATCC 27244 (bacteria)
Gene: HMPREF0023_0548 / Production host: Escherichia coli (E. coli) / References: UniProt: C0VHC9
#2: RNA chain
2'-5'-Linked Cyclic RNA (5'-R(P*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1490 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG-3350, 200 mM lithium sulfate, 100 mM imidazole pH 8.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→49.21 Å / Num. obs: 217277 / % possible obs: 98.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 39.38 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.042 / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 10452 / CC1/2: 0.55 / Rpim(I) all: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.21 Å / SU ML: 0.2286 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 2000 0.92 %
Rwork0.1854 214812 -
obs0.1857 216812 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21078 0 370 1490 22938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004421932
X-RAY DIFFRACTIONf_angle_d0.76429729
X-RAY DIFFRACTIONf_chiral_restr0.04773292
X-RAY DIFFRACTIONf_plane_restr0.00353751
X-RAY DIFFRACTIONf_dihedral_angle_d14.35527904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.3121390.265214892X-RAY DIFFRACTION95.7
2.15-2.210.2831410.249515156X-RAY DIFFRACTION97.22
2.21-2.280.28441410.238815126X-RAY DIFFRACTION96.77
2.28-2.350.25171370.222614757X-RAY DIFFRACTION95.1
2.35-2.430.22131430.205815365X-RAY DIFFRACTION98.23
2.43-2.530.24461430.201415335X-RAY DIFFRACTION98.4
2.53-2.650.2371430.199415380X-RAY DIFFRACTION98.56
2.65-2.780.26571440.198315433X-RAY DIFFRACTION98.76
2.78-2.960.25621440.200515465X-RAY DIFFRACTION98.83
2.96-3.190.22321440.196815439X-RAY DIFFRACTION98.87
3.19-3.510.22191420.192415388X-RAY DIFFRACTION98.17
3.51-4.020.1961460.168815554X-RAY DIFFRACTION99.37
4.02-5.060.17551460.151815679X-RAY DIFFRACTION99.5
5.06-49.210.20891470.171815843X-RAY DIFFRACTION99.29
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.786415376223-0.6175478702470.2907639856332.08157858804-0.08134326750561.672011343420.05304555529640.09325783743060.0959610409787-0.071846412566-0.0244535761319-0.187954724144-0.1931809150260.0389061091617-0.0265953080080.237501345677-0.01745509749230.04906509633410.337748820801-0.04255136516720.29419256399433.4709929851-12.923619293222.6434167748
21.847465006570.606169872971.403493960680.7083962856840.4223628379281.914197108610.06710821514650.346458751454-0.253847541013-0.1454869332250.0311885607692-0.3036294474690.1748097758920.431152744046-0.06715559499130.2636638447160.04737691785610.04982384400190.365726485437-0.02739824201440.42344343767452.8543447861-26.87548849235.875807616
33.19517487187-0.897684667420.01037508035434.623758233810.2053087251463.20833623839-0.0644837293805-0.43212251599-0.1211780982550.750153475553-0.0142601279778-0.5177938092020.208636601660.2896142667530.09987104911530.292182713224-0.0233938231908-0.09382201109190.4420752885390.09505138058130.45278192382964.8684078341-21.704207466263.2382831481
41.87466938186-0.522854416337-0.1703050489010.625316979842-0.08641021195862.269857652750.07147963752850.1866144928940.0522175028359-0.07012819882420.0105704725769-0.110096060763-0.1141320503560.186864670796-0.07150478469410.242498072795-0.0252141570283-0.01501641096130.222965195494-0.04469674087690.33581852942631.326385473-1.2237951415552.5777670923
51.66669972238-0.0667622309797-1.37965613781.100576147520.6792839888476.593230225160.158414027235-0.1582454658970.1473927627210.1131510096650.0683462720148-0.269263677312-0.2796117811980.584865119537-0.253616238810.284076019792-0.0429021705278-0.05026713906710.199690836945-0.03005585659630.43673040263433.39760765633.8387592416259.7737190477
61.86930616725-1.439762098841.143459169771.78463347743-1.205594079882.07211375899-0.174721508008-0.2248533626990.2055829843730.3951260650070.120626610743-0.0741564991241-0.523480663495-0.1927056317230.04451580303450.361918510363-0.001530178520820.01864564969490.270987024035-0.04818513001510.331399275879.4207358223111.145702800465.6623469161
72.18846339244-0.550710387758-0.8454097950862.930380619310.04128064237312.34197543365-0.128363129397-0.1734890377940.1349403906750.4258966494470.3488475257130.578820124714-0.788725992945-1.32094232347-0.1487675852910.5980258962510.3584462317810.1230362257350.7377630147150.04006711706680.483897522351-13.087547361824.629021087458.0936512151
81.576047770820.2145213534880.5768302054681.497035257750.7482863266972.35978535041-0.0237942827154-0.01531325814680.0131273859725-0.04369149911310.067765725793-0.0528135565182-0.0320689868580.0409380444965-0.0419314930370.2367898387510.04220343962040.01679952226430.1899793966670.03420815145320.175535367215.599630692542.9556781974330.3113535814
94.914326242470.6026062388042.419204981871.83344730470.6914414942752.7598052059-0.2908280446580.1061436345570.401307625096-0.164715621230.194438127153-0.0568515972905-0.3742403845610.04984399101170.07078746158310.3394863260150.01374599851360.04815893973730.1943753919150.05533861111240.2047958927098.401925097610.620228857125.6254551076
102.68659860728-1.22814351115-1.112372315731.128390251720.5427146895082.164099445180.2276258765580.5940487477580.00841885855174-0.411087846752-0.1709822172490.0564396501937-0.0625314687569-0.266980392719-0.05978876229230.411871595509-0.00534304195988-0.03198867907760.3139161543780.01385020190370.2183359037782.56828448631-8.069696275025.33390212185
112.138362189610.351321629235-0.07548629522072.31382831480.3244254857412.593089698450.4792402091171.32208185021-0.710081841653-0.995888552164-0.310908824344-0.1274922653570.3197367660770.228632590268-0.1471033456670.9063322584470.205584045387-0.03891778073670.955156011845-0.2382120015460.44978895505216.7026690699-21.4220233328-13.5317776828
121.12936371452-0.3776357431520.195754320491.995027715080.6955561889891.409401691430.05883349296670.0638135314928-0.1920334127250.0767651044851-0.05732929713370.05393915765570.165054452398-0.09272920495150.006012605586880.1929995574-0.04496153107110.01793571587890.3274068251480.01459192216570.259948575104-9.88002056913-22.93555275248.7362564015
131.60007170179-1.0746685013-0.3203485544443.426680451511.112587276091.821177103530.06448516503120.105091324206-0.122447913408-0.0182966197439-0.1847168827860.560120711440.0421440988887-0.4129249945880.1076758364320.176214036679-0.07227020980760.03033922812470.3669846650850.04701625038730.29505837158-17.1640174322-20.144531620553.2588452667
140.819832285995-0.7115496907250.7736661187250.942174415595-0.6356357918712.11532704953-0.0095117047186-0.176774673211-0.01477555530370.2765167585710.00698625656240.167492258088-0.0696610061191-0.2365115805110.01403117595390.29215747811-0.08729726295950.05967947415350.3144602239460.002270387905810.298302197392-5.01449001695-10.068127120473.5516681866
153.39951486266-1.13751177299-0.004834781216153.899111945610.3107487852922.52954149875-0.183309029438-0.7554527145670.3544075416280.9315260265980.199059059845-0.568807094779-0.1228854221350.457604063733-0.02055334722750.600427588739-0.0652624398463-0.08877763484190.542317642671-0.03039956530820.30967344436411.2300985944-14.167062832995.0244542478
161.72986192464-0.42533278459-0.4561944327870.9376577939060.5206208900771.045031017860.0107095066080.0313680270755-0.0197147905694-0.06933877093780.0066516299528-0.06320130451830.081780000215-0.0753946857826-0.01751417180240.2800511680990.00502048407998-0.03171223886050.1695512405870.03906375707570.23072818037122.8664704029-31.422499420960.5157355719
172.92887244645-0.0616473665987-0.1781680515661.032524718870.539148594322.02459092522-0.0579217788063-0.0101189905008-0.3960457375790.07845167429640.03068923450580.1869268245130.45251319941-0.3861714460340.01056924052040.395032091322-0.0681335120341-0.01256902002720.3045290459020.05209770037610.360257187168.75735377213-40.896553359561.4118508529
184.1104348986-0.08505422445381.427276959160.887139630383-0.7201946491990.984498853189-0.0458547385261-0.568377582806-0.5701027014620.4790963430120.092033857367-0.06603131817970.2325999489240.024014723334-0.01321226255060.5937172248010.00554377167143-0.08659613444390.2962095470950.1099435145430.3984563250436.486829128-41.39606104371.9146357923
192.34889024093-0.07040054001620.2805919631411.686546107390.6251624079663.17319394711-0.0168839740945-0.0927220121732-0.07075264279320.195818164581-0.0219090081472-0.4497248443760.253986707430.458725038387-0.02496456319510.2999921510740.0425443954399-0.02354736912190.2831972254550.03596492037680.34643468829943.7721517376-35.178221388263.4617617601
202.1118090770.2238635415281.053991536591.315048866361.273310566112.907329914790.1452646767790.187168039185-0.6952351680870.06191289042730.00233008733692-0.1879180564550.5606247509210.294273948702-0.1892233502330.4805273692160.0774532890007-0.01743841448770.305217887935-0.01829776250850.46739875541234.5262062909-50.720945349941.3767792216
211.048164035160.171914964827-0.06691208532521.463829474080.9992302162081.455305805220.1750533524070.742104999009-0.993671570709-0.1489162143990.211560094397-0.5017648345050.9049309023370.82663122994-0.4107070802760.9576956135560.337256433321-0.06182398542250.997268425268-0.3795862517341.214123902647.8972718255-64.224707709630.6284381128
223.40699893471-0.3582379168941.433319294781.71147912157-0.2179609568653.29135203484-0.01803262306650.757595414466-0.805099778777-0.3076380189110.352068607379-0.6813293993560.45941687270.834792121379-0.3827429553330.6874459970460.1537582183870.05346195022420.704426201079-0.3201363804140.75441738386140.3121667217-58.23548445227.9270276344
231.57535500634-0.2664723033320.3418223017310.357311440433-0.5273682876011.985276525480.041676079948-0.019370994001-0.09804417620030.0940260844038-0.00391676687502-0.004148112758610.213735955811-0.0505816714862-0.06158760755460.351100750342-0.0244413733044-0.01287380893490.225041482461-0.08303905601570.27114550923710.7011397653-40.547560140627.9747855198
241.07181232571-0.1566364680880.2018512824190.89052997074-0.3336655771285.60800374195-0.0192989857120.110981691513-0.268097284992-0.0704687443320.1144214204130.05293129970090.90397388757-0.2680475524030.03348937832170.456172710748-0.0884930886831-0.00548762567970.290277347337-0.07454996505750.435522619945.34797312431-48.409801060328.5406107415
252.5965998049-0.880411017159-0.8473971618080.7068252756370.6194831869911.458934120130.04975741179910.478993291748-0.198891045794-0.16442835983-0.1212124289450.186566747340.159753849663-0.4289338084850.06108019537360.409237926763-0.0683343751917-0.05870739475260.428925873302-0.03407325364330.368472747461-6.80522413668-30.476565468414.8645894176
261.16565049190.1026494922370.1770499629680.552955764945-0.6496335639481.93558633331-0.0117287913250.559666478184-0.0483979934032-0.2204866946410.1209575980250.827198353594-0.144783292555-1.67472138492-0.1404664053510.6897643566640.0123721061402-0.170597627661.67053189660.1141432728040.882833934334-34.1088834705-20.34340266211.3169775743
272.73130169813-0.60647494507-1.106137477280.981721617991.114669086674.532141272830.1616758266010.7967397728390.349670533208-0.272996934070.04560535983310.3380787623-0.16929300853-1.30157776839-0.2841854819860.3497869844480.0295282224684-0.06749363917510.9458946946350.121131138310.629990299611-28.8144026242-18.749502233719.4800140097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 342 )
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 462 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 147 )
5X-RAY DIFFRACTION5chain 'B' and (resid 148 through 189 )
6X-RAY DIFFRACTION6chain 'B' and (resid 190 through 342 )
7X-RAY DIFFRACTION7chain 'B' and (resid 343 through 462 )
8X-RAY DIFFRACTION8chain 'C' and (resid 13 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 13 through 147 )
13X-RAY DIFFRACTION13chain 'D' and (resid 148 through 189 )
14X-RAY DIFFRACTION14chain 'D' and (resid 190 through 342 )
15X-RAY DIFFRACTION15chain 'D' and (resid 343 through 462 )
16X-RAY DIFFRACTION16chain 'E' and (resid 13 through 91 )
17X-RAY DIFFRACTION17chain 'E' and (resid 92 through 166 )
18X-RAY DIFFRACTION18chain 'E' and (resid 167 through 189 )
19X-RAY DIFFRACTION19chain 'E' and (resid 190 through 234 )
20X-RAY DIFFRACTION20chain 'E' and (resid 235 through 318 )
21X-RAY DIFFRACTION21chain 'E' and (resid 319 through 415 )
22X-RAY DIFFRACTION22chain 'E' and (resid 416 through 462 )
23X-RAY DIFFRACTION23chain 'F' and (resid 13 through 133 )
24X-RAY DIFFRACTION24chain 'F' and (resid 134 through 189 )
25X-RAY DIFFRACTION25chain 'F' and (resid 190 through 318 )
26X-RAY DIFFRACTION26chain 'F' and (resid 319 through 415 )
27X-RAY DIFFRACTION27chain 'F' and (resid 416 through 462 )

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