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- PDB-8oiy: Crystal structure of the R15908H missense variant of titin domain... -

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Basic information

Entry
Database: PDB / ID: 8oiy
TitleCrystal structure of the R15908H missense variant of titin domain Fn3-3
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin Fibronectin type III A-band
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy / mitotic chromosome condensation / protein kinase regulator activity / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / actinin binding / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRees, M. / Gautel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationRG/15/8/31480 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Structure determination and analysis of titin A-band fibronectin type III domains provides insights for disease-linked variants and protein oligomerisation.
Authors: Rees, M. / Nikoopour, R. / Alexandrovich, A. / Pfuhl, M. / Lopes, L.R. / Akhtar, M.M. / Syrris, P. / Elliott, P. / Carr-White, G. / Gautel, M.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Titin
B: Titin
C: Titin
D: Titin
E: Titin
F: Titin


Theoretical massNumber of molelcules
Total (without water)69,8046
Polymers69,8046
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-15 kcal/mol
Surface area26230 Å2
Unit cell
Length a, b, c (Å)52.480, 56.030, 56.090
Angle α, β, γ (deg.)60.060, 70.160, 65.620
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 11633.986 Da / Num. of mol.: 6 / Mutation: R15908H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10mM Tris-HCl PH 7.5 NaCl 0.5mM DTT 0.1M sodium acetate pH 4.5 0.2M Lithium sulphate 50% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→47.11 Å / Num. obs: 25781 / % possible obs: 88.86 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1163 / Net I/σ(I): 5.36
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.3238 / Num. unique obs: 2523 / CC1/2: 0.719

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.34 Å / SU ML: 0.2461 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.7752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 1367 5.3 %Random
Rwork0.2061 24410 --
obs0.2084 25777 88.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 0 262 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214619
X-RAY DIFFRACTIONf_angle_d0.50936327
X-RAY DIFFRACTIONf_chiral_restr0.043716
X-RAY DIFFRACTIONf_plane_restr0.0039839
X-RAY DIFFRACTIONf_dihedral_angle_d4.7131646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.281300.23182393X-RAY DIFFRACTION86.49
2.18-2.260.28321050.22992144X-RAY DIFFRACTION77.95
2.26-2.370.27881390.22222508X-RAY DIFFRACTION91.5
2.37-2.490.3141680.23422526X-RAY DIFFRACTION92.86
2.49-2.650.3111510.23482529X-RAY DIFFRACTION92.22
2.65-2.850.29271640.22732481X-RAY DIFFRACTION90.64
2.85-3.140.25671080.21992411X-RAY DIFFRACTION87.07
3.14-3.590.23991310.19052347X-RAY DIFFRACTION86.07
3.59-4.520.22511410.16542591X-RAY DIFFRACTION94.11
4.52-46.340.20331300.19742480X-RAY DIFFRACTION89.72
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)
11.678451835930.3978955062390.4560311301772.332910079611.099565393061.783416618350.0983644011169-0.0417382290539-0.1054411980630.200487220777-0.0238196722733-0.0185957678675-0.08108196291270.0321286330495-0.07394963373840.1834966051520.0198828007836-0.006808619058080.1389506368680.02289680671690.131631386049-100.446170744-35.9812256361-9.84867298906
21.06146976770.9262248034841.911781450911.44112269740.6131801342815.275104426050.248006188468-0.0119875742833-0.132387765770.452416815827-0.06616480130850.3637779578430.98680248752-0.739386855099-0.1234519052370.290658338051-0.08313139748740.008196876929610.2584177166210.03412660376440.434957496789-108.70562344-45.9734101103-4.35055164084
30.6827707637540.820021915486-1.30575721722.85995550813-1.281687875682.597719206630.198087914301-0.322579413737-0.6000016861650.361895540179-0.0480481075175-0.4966977281380.1252668108290.5276617608990.2293016865820.1277856800120.0127515332917-0.07477964900420.1915191076920.01236369494080.245526834154-94.6489407324-41.7280511357-7.96833738902
41.776590250831.662612009130.3790240070652.984078244880.262721128511.771498954830.0675857999702-0.0523950663904-0.072675743910.158216334947-0.09784427647980.087621437814-0.00155249554928-0.112017836013-0.01396539125920.1323149875850.0184586957831-0.00214960243950.1097422796050.007704112383820.120469931192-105.86560081-42.2022931772-10.1836249988
51.32184591955-0.2699300805180.4028513830911.84715561588-1.030482504471.336841386530.139104929003-0.21534557844-0.0726506901769-0.295442676795-0.0732098666661-0.1422553089530.465097203976-0.180870844935-0.09308933811330.1542593993060.02262474007980.02085144197770.080335009011-0.0131801728620.125956716312-94.4863018308-19.9792778984-20.5433246798
61.49252333196-0.00991844793669-0.03727133587341.38584451242-0.8984232514822.16708056910.01905920243-0.1365748547880.021128454157-0.0160063835883-0.0432862028062-0.0896746031615-0.3119005790520.01883953774830.04036845947590.191949546472-0.00286018241793-0.005296854277180.132415662175-0.02753862154490.181081557483-95.3392483359-14.1425040681-22.9086615657
71.377691604690.2354342705341.271953793383.38989698688-1.583647160342.143229539770.1934771353540.05480918915520.123523559356-0.385327525884-0.0499097978449-0.2515680542190.186654387640.5449709405020.06615761344370.131741206143-0.005329363585480.02165566509240.245052208849-0.05915441066510.183742416649-86.9094613546-18.0506962124-23.3077129645
80.726606995230.845372763090.3520293421661.372591068080.186265417033.08433381352-0.0227083570117-0.0629317890921-0.05861457004180.01687573102450.0381758993239-0.0574158912869-0.33160683341-0.254553401616-0.0062156052390.1416564744280.0265838882527-0.0159318623470.0820132296356-0.000426981443270.130217584706-95.2376510265-13.7933956589-18.4905753522
91.221175895390.0541798783662-0.1728100343650.383905748990.496687905620.6951712496670.0612077244396-0.073344440792-0.05648924604890.150293930144-0.0228938558988-0.0796275765954-0.06354130657210.2750115197620.5408499735370.363598233074-0.00776244023485-0.01695645918930.2013917106410.0410218348024-0.013917187055-93.2326488048-20.5353043154-6.72653416683
105.278242986323.793911914580.02584514599965.2297869766-0.05709600572781.978518908670.58614273302-0.486242737924-0.01073450252440.547947879014-0.492217949348-0.2587104048610.1075920591110.034518806114-0.09003927253330.2045878529030.000289696220877-0.006715891602710.1665052551740.03115232290220.211673044497-112.265829542-39.6460222636-25.9901887691
111.2146901537-0.327588832347-0.04096862372261.2682836389-0.7866537770942.502883046090.189556289506-0.0563342144405-0.0187867204404-0.115964638695-0.197590524136-0.07445461174370.09035830670550.2366270107720.009391525640410.1638129771230.00760818729293-0.01708286670560.119607232615-0.02722073460650.175773018147-102.120887116-36.4766948781-31.011814846
122.79275246839-0.2711467315071.201565938661.93158228267-2.431413892334.88423250449-0.157791449454-0.04186744866980.138574046971-0.7954010657440.217664871836-0.6807640525240.154832103365-0.296303273401-0.04514340094930.379527391037-0.03407769101560.05282611793840.122166133953-0.02714563594460.199524636725-107.489812506-35.6027135511-39.073226193
131.42469706870.5848876202240.4382977054580.4095782691350.7388575459321.98961168069-0.1220330795730.4350152264530.205068850476-0.480267924431-0.09610957357550.125813018316-0.3536360270540.128933244073-0.2309258843660.6209829759740.0236421434441-0.08776833546860.4306634749230.04395432596590.0717441548046-110.352643637-32.1871887791-43.7650158359
141.303416996270.1831646140330.9115788439644.97936959388-0.437872933731.08095669564-0.05551419953740.194816528-0.594390748398-0.691897036541-0.1667872789180.08339110891970.1554970369550.298218338554-0.1626781137970.1751660303440.05141583980930.03351176013530.224556444295-0.05082689035090.229070427633-100.177118695-40.7860260863-36.7049234611
152.95175760831-0.839457966960.1117417217552.835556875970.25854573553.56410757219-0.03880763770880.4657580934980.369998320243-0.2602081073640.207225447084-0.440183257213-0.2178425177620.6195006679630.1605284029960.335708504138-0.0134091700578-0.04446284542090.224612781022-0.005964740344630.17812057001-100.21717547-24.8595268819-47.2086511463
161.570115095771.169737631160.3161299765263.2089666204-1.286280665322.55872865138-0.0146670166170.09965518412210.0304521479404-0.05534402276190.002484969677020.0429927084636-0.0502027280879-0.140587125716-0.01986317165370.1680635557810.0204426434335-0.01089069737390.1386446025140.0002898916691730.117084567313-107.605589059-32.5939094527-35.3548780349
172.43044240040.9009202958930.05190228346121.512316083441.020750701261.52987629528-0.0377872769558-0.1583552900130.2006638906560.00264482373209-0.1091599115510.131138092962-0.121853334753-0.07807175625590.1106560368180.1821431948740.0251914282081-0.03421964311460.10497400335-0.007948773440860.180702605232-120.192137167-12.2731741246-25.4586653569
182.478468433621.322149350380.3421747105352.43112697252-0.3022479033321.23554673304-0.06728690986360.242024748603-0.097410948735-0.581553906664-0.117154392957-0.139119903445-0.188445729935-0.3716379963380.07398245882560.275409801740.00929361839346-0.004983504293360.1838128683610.01480545096370.216081359692-120.551780337-11.9395063873-36.9295051533
190.9928278530880.07636042554470.5579362498080.8966560511150.2524056199583.01597746655-0.06687208156920.07164677261760.0690870336151-0.391485258453-0.1827319658560.168994682943-0.02607795238680.009558950109260.3011530813020.151289316150.0400657287257-0.02539493934080.138322924769-0.005425916809790.111700696791-129.182966908-15.7461250093-35.4627135723
201.453607777770.6463829420980.1945865429221.755228866121.283143843671.61020948778-0.003590741601090.08995743274570.0519034408363-0.03644137630690.0310000445984-0.0486489493901-0.006080304952050.0649698728155-0.03122454073240.193530136682-0.0194123627643-0.02240162839740.1688899028020.01363731815640.102579321565-119.525668488-16.2146058202-32.2161636713
212.89321263990.1674597349580.0495484376822.80419745629-0.7275919780961.827890886030.0769556497487-0.1722984091960.0225099703944-0.3431352268120.2473471602230.1680774817310.102467303744-0.240644277543-0.03865537952610.11258875583-0.0526518134959-0.01166495669380.1516426835410.02948563478250.125551613436-118.348681853-13.0802272639-8.15623966917
222.31150484771-0.07065127169230.2996574496212.04376475142-0.7657697870421.937333861520.0599134424042-0.237486122411-0.01873155087550.210702703749-0.0427017068820.001612183249460.108311967831-0.1121582262990.01347797887370.221683767621-0.00990028953652-0.01577296245310.1841164615460.008241929687550.119185235092-117.610647082-19.9718988486-2.5307597177
230.907459149731-1.416123654581.525876096585.13168556919-1.594733474582.78801000692-0.08956067985860.06270716174090.8353418602370.593950693101-0.233390866707-0.751101916931-0.3495038439530.243859845585-0.04782624184090.358737293996-0.1318962636690.0154252751810.259696245323-0.05863216065530.401495538448-108.136313993-7.77448563187-0.855904797679
240.979989321789-0.7421476245340.6129194975292.727526683320.3982280644121.312355753530.0539155339808-0.7271285685490.2641991885531.013295514160.2028028532210.7674671984910.132495939713-0.09003432804210.02388430734930.263718370622-0.02679627331420.100096267150.251870542183-0.0259285447420.359932123214-122.348118193-11.2195109888-0.328814544565
252.564698166450.700377769440.1416916692412.82317228151-0.58754467711.673470132740.02020739532-0.0286713377693-0.01289443064070.0652973869069-0.006652749618640.01966433879930.1768191422370.0553909522309-0.06037345065090.1504645853410.00847332361179-0.0275234893410.137163169641-0.002817090025340.14280067212-112.535387965-12.9888655152-3.9555975179
262.20659022007-0.5562308757810.6379414134823.242252102640.6022498114220.8804332757760.2885115822990.5391490968870.251627425127-0.419219205851-0.582838067993-0.06895521388890.0512666654953-0.08079457862960.005344750486880.1601007034740.04852341983470.01561636659950.1511938529910.008619377250430.183282646642-114.683615841-3.27026896844-14.5251499731
271.36649629639-0.310091425947-0.178892997451.22996888462-0.02355218695982.145239334150.0384770470719-0.109474250179-0.107032609451-0.101090635538-0.14640608705-0.0122149856627-0.4114684596240.1625111899470.03655361027580.1191615586160.0102883491986-0.02847165625960.09132319686310.01650073040620.12194528808-127.607357717-30.9683023328-15.0750539853
281.05540978232-0.5426726848450.2085700880752.4111256772-0.2767894898222.14324144172-0.03062928844360.01989970878480.0409986749578-0.07395878840720.09685553600530.2091452389590.553527119295-0.119262620472-0.01581833024930.172180690828-0.0413478791472-0.04652346218740.175972875815-0.01658393988220.172298932916-128.066456959-33.2523818349-22.6716701797
290.3384801787620.00428251060194-0.3620997758981.525671200650.4104617183050.4998883276250.0665978141675-0.16095243536-0.203373927090.9245179887690.627493553616-0.520637373231.164366013460.138483329196-0.07943354270870.6720078204450.26920891248-0.2739962146320.574042804326-0.2846295952520.554831320423-122.203304629-46.5823511657-6.28669304637
301.27211439341-0.7042076454450.8516329987631.99262261613-0.4675722968432.731530236750.1890991659650.0898572820667-0.322622547059-0.103252532864-0.07598964530030.0533980849420.6185169046960.0348393799858-0.2199361981490.199571683894-0.0383340519834-0.04009402153910.2353396660340.07209671005160.197846783512-132.69889225-39.6911903089-17.134554724
312.00797040549-0.0467002203431.890203703273.07540470347-2.455059530744.29652342989-0.0513227915399-0.4038714336950.1117562553440.2825830025630.08686548624830.2424539657090.130642791027-0.618708508124-0.5215321122930.2159871720470.02348629825150.05571389131930.1355048378110.02870902767530.185492623463-132.680032635-34.4811940119-7.67190444707
321.30607204225-0.1046376765120.7191379587261.51713815586-0.9198358871762.99712163791-0.01634863913760.157651480523-0.08023365899760.0423341082537-0.0127649919805-0.1247237310950.3966167811950.212121453687-0.01044364455260.181441743429-0.00851123586651-0.02126594747630.1159563942-0.01709503943450.165296118171-125.079201417-35.9870862273-14.9752625521
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 46 )AA3 - 461 - 44
22chain 'A' and (resid 47 through 56 )AA47 - 5645 - 54
33chain 'A' and (resid 57 through 68 )AA57 - 6855 - 66
44chain 'A' and (resid 69 through 103 )AA69 - 10367 - 101
55chain 'B' and (resid 2 through 25 )BB2 - 251 - 24
66chain 'B' and (resid 26 through 56 )BB26 - 5625 - 55
77chain 'B' and (resid 57 through 68 )BB57 - 6856 - 67
88chain 'B' and (resid 69 through 93 )BB69 - 9368 - 92
99chain 'B' and (resid 94 through 103 )BB94 - 10393 - 102
1010chain 'C' and (resid 3 through 12 )CC3 - 121 - 10
1111chain 'C' and (resid 13 through 38 )CC13 - 3811 - 36
1212chain 'C' and (resid 39 through 46 )CC39 - 4637 - 44
1313chain 'C' and (resid 47 through 56 )CC47 - 5645 - 54
1414chain 'C' and (resid 57 through 68 )CC57 - 6855 - 66
1515chain 'C' and (resid 69 through 75 )CC69 - 7567 - 73
1616chain 'C' and (resid 76 through 103 )CC76 - 10374 - 101
1717chain 'D' and (resid 3 through 38 )DD3 - 381 - 36
1818chain 'D' and (resid 39 through 61 )DD39 - 6137 - 59
1919chain 'D' and (resid 62 through 75 )DD62 - 7560 - 73
2020chain 'D' and (resid 76 through 103 )DD76 - 10374 - 101
2121chain 'E' and (resid 4 through 25 )EE4 - 251 - 22
2222chain 'E' and (resid 26 through 46 )EE26 - 4623 - 43
2323chain 'E' and (resid 47 through 56 )EE47 - 5644 - 53
2424chain 'E' and (resid 57 through 68 )EE57 - 6854 - 65
2525chain 'E' and (resid 69 through 93 )EE69 - 9366 - 90
2626chain 'E' and (resid 94 through 104 )EE94 - 10491 - 101
2727chain 'F' and (resid 3 through 25 )FF3 - 251 - 23
2828chain 'F' and (resid 26 through 46 )FF26 - 4624 - 44
2929chain 'F' and (resid 47 through 51 )FF47 - 5145 - 49
3030chain 'F' and (resid 52 through 61 )FF52 - 6150 - 59
3131chain 'F' and (resid 62 through 75 )FF62 - 7560 - 73
3232chain 'F' and (resid 76 through 102 )FF76 - 10274 - 100

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