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- PDB-8oty: Crystal structure of the titin domain Fn3-90 -

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Basic information

Entry
Database: PDB / ID: 8oty
TitleCrystal structure of the titin domain Fn3-90
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / Titin Fibronectin type III A-band STRUCTURAL PROTEIN
Function / homology
Function and homology information


sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / protein kinase regulator activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / protein kinase regulator activity / cardiac muscle hypertrophy / mitotic chromosome condensation / actinin binding / Striated Muscle Contraction / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / cardiac muscle contraction / striated muscle contraction / muscle contraction / protein kinase A signaling / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / 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 / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / 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: 1.9 Å
AuthorsNikoopour, R. / Rees, 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
DepositionApr 21, 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


Theoretical massNumber of molelcules
Total (without water)45,9234
Polymers45,9234
Non-polymers00
Water4,990277
1
A: Titin


Theoretical massNumber of molelcules
Total (without water)11,4811
Polymers11,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Titin


Theoretical massNumber of molelcules
Total (without water)11,4811
Polymers11,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Titin


Theoretical massNumber of molelcules
Total (without water)11,4811
Polymers11,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Titin


Theoretical massNumber of molelcules
Total (without water)11,4811
Polymers11,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.080, 137.461, 51.546
Angle α, β, γ (deg.)90.000, 104.020, 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
Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 11480.870 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30mM HEPES pH 7.5 150mM NaCl 1mM DTT 100mM Sodium acetate 200mM CaCl 20% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→28.32 Å / Num. obs: 25557 / % possible obs: 96.88 % / Redundancy: 2.7 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.08891 / Net I/σ(I): 6.15
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.4023 / Num. unique obs: 2190 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.32 Å / SU ML: 0.2476 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.9301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 2410 9.43 %
Rwork0.2009 23135 -
obs0.2056 25545 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 0 277 3422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633222
X-RAY DIFFRACTIONf_angle_d0.62214394
X-RAY DIFFRACTIONf_chiral_restr0.0514513
X-RAY DIFFRACTIONf_plane_restr0.0067566
X-RAY DIFFRACTIONf_dihedral_angle_d13.27751220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.31711150.30451056X-RAY DIFFRACTION76.89
1.94-1.990.33291350.27141345X-RAY DIFFRACTION96.1
1.99-2.030.28391330.24341330X-RAY DIFFRACTION95.25
2.03-2.080.29561470.22741369X-RAY DIFFRACTION96.07
2.08-2.140.30311320.2291327X-RAY DIFFRACTION96.88
2.14-2.20.2821390.23021369X-RAY DIFFRACTION98.37
2.2-2.270.28891490.21781402X-RAY DIFFRACTION97.36
2.27-2.350.2911380.21991381X-RAY DIFFRACTION98.44
2.35-2.450.29971430.22531376X-RAY DIFFRACTION98.32
2.45-2.560.28071510.23151378X-RAY DIFFRACTION98.33
2.56-2.690.29291480.2221391X-RAY DIFFRACTION99.55
2.69-2.860.29911450.22561412X-RAY DIFFRACTION99.05
2.86-3.080.25531430.20731396X-RAY DIFFRACTION99.23
3.08-3.390.23351510.18851367X-RAY DIFFRACTION98.89
3.39-3.880.20931480.17461399X-RAY DIFFRACTION99.36
3.88-4.890.20081480.1471421X-RAY DIFFRACTION99.62
4.89-28.320.20461450.18021416X-RAY DIFFRACTION99.17
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)
13.81270941033-2.011024380942.448519075173.0991051709-0.2554244676556.87767952990.183708915350.201645712247-0.193085453478-0.000804938834463-0.01937636039060.1820890286280.5954336689430.6912745291930.02297318012440.2019867498090.02394878260930.03542995158790.185172386087-0.04458720582220.251102272825-7.23376806926-42.516683893813.3525780984
22.50644367038-2.767095447771.962146304743.61159682274-2.417250457851.796820119270.4582209041220.438447022082-0.453331540957-0.265466807892-0.5402671296221.0925928671-0.04124244130220.4830495750340.06101383304110.1891288922170.0504963698250.05210082039420.290781391916-0.06617384763870.270675417959-23.1832832992-35.239142481.81243972271
32.34361918953-2.595029066652.827983808522.92695666039-2.007351232361.77925444480.177902666101-0.14167135729-0.0964867452983-0.4164017647680.2231507446930.2980439642590.305827142152-0.325199040135-0.3202815180850.152607084188-0.02222714335440.03483720109940.1933454879670.003950522892530.252245275994-16.9614956751-39.384608720711.2408447096
40.9014843954931.37749262285-0.1127294408045.05034368985-2.627381973783.778372304130.01290718772960.007588695672480.0161663175709-0.0354658349377-0.08966613475080.221870200693-0.3535326286070.1851769822450.09350956808660.1324359973410.03113655692230.001189350211710.2097362744610.001167978873960.160319108652-12.9465501598-25.818486231511.2144997174
50.847154208287-1.389900713810.9930141552893.96757070395-2.226382895292.82714097272-0.05555945230550.0134349941909-0.05734848547660.1435550442840.0226992300420.143173348651-0.187232368949-0.1238059406120.001921118935280.1623057148010.002280043558770.04278006381490.182337320666-0.02019842558970.13256045871-19.3835235175-29.988636915711.3974867148
63.3146739538-0.9057195103110.8924527418884.47468330183-0.3275348619891.38267574287-0.1003897416860.05747504259880.1693747212181.12481307831-0.421651655697-0.634971400237-0.8943941996621.12151733462-0.04996733339190.124287746116-0.05053411127360.1108281710050.12601950395-0.01246102364250.194356698181-7.31477283017-38.508540208117.5285661637
75.89580864467-0.8712995438141.596587685572.27843139548-1.483826878383.55400889863-0.1621274393741.21372520741-0.0800081470246-0.248559881377-0.0791993325257-0.03388549375950.4944476490870.06509270351520.1050701724860.326388203406-0.02182007794030.08664049378840.242413207649-0.01404439759940.170041636288-20.5123937981-26.1866126772-1.20530804552
81.426566836050.6174232498580.7858830226231.480586741040.7867951248662.606039393030.3496589134470.2211971631930.0798649806413-0.3476556587440.08494424145371.046927986180.8920387517960.1640791544340.853078202820.2886909082330.0616421881939-0.04491526681080.0839540514714-0.05432358012710.257224669691-18.8700136143-8.41919026024.55395465221
91.3727295389-1.78874938726-0.3589784309943.87461589444-0.2134988927873.134971784220.0279288343962-0.1117264464140.1950672876010.5134021733680.284887180995-0.779226361125-0.7345057224940.2023904689070.06248706674280.218367050265-0.1040313439840.1008241930370.228303826970.003649632696960.172390238333-12.08653757415.8603731237517.4486127442
102.350437067471.959058607860.3551264668584.253252296260.02437623953683.091154406460.02501253998340.316535690868-0.3898443607230.04019657466420.136127796477-0.4229471289880.138320682741-0.267795948354-0.1595316839920.1865212530560.01966655729310.05681778178990.2870773720030.01960607025920.210238053051-13.268552224-10.80515869292.89397252884
113.07324724018-1.74855080254-0.6001274592035.279900717730.297752281893.106027307180.2728570347090.07078544214230.195753926173-0.296466238954-0.067243328271-0.0591460441836-0.1680341120360.0796607979078-0.1542054014660.211189190413-0.04047631117830.03945108161310.159231826641-0.000709749503120.151769319468-16.17375546286.040090609714.54981848793
123.15068791137-2.04904918333-0.6464448253374.71492105612-3.260587302955.48520634627-0.0900537523893-0.49184704860.94296483146-0.208180585148-0.919171401792-1.27476508418-1.09388175111.27209804561-0.4534784592550.534586010858-0.148748055150.1538578968490.2313817012440.150963984034-0.00166449939421-8.61019711896.3028821354811.2526653426
131.57053217566-0.185780123147-1.36020480962.454927807321.809257449353.536825237570.091991107258-0.06469607133270.221286816872-0.104758576011-0.03990301595650.118493256251-0.6099047184840.182258212338-0.1586276260750.320069723168-0.01230760674320.04034559510480.16825968120.05584061521790.162319529808-18.23548897089.0106886817210.2723790098
142.90641083046-0.14648227968-3.836207538514.37837049984.091770714539.2780182942-0.05000246296840.641215375102-0.3640380637710.07472188856230.0630542110880.4343485010241.29690054898-1.31890226036-0.01658375384040.302477817510.0618685714255-0.04205385659010.1534128447280.008402381204370.177923055258-17.6892731154-5.39727248327-2.04374206535
150.42532339636-0.590323478131-0.7340345647512.903958645521.99159429586.579830227380.0274604433937-0.329557019932-0.2673340343470.199425911659-0.1749939324970.2079942877720.0805575767558-0.1126440941370.2498529432370.192906937304-0.02918922864630.08465128549620.2882623237530.03063503167710.345103159962-19.57576754799.698784100919.9455979682
164.42707873534-3.8075947255-3.993569670384.849293325214.276056279048.478212086910.04925470714140.848305365937-0.3402303751-0.156502389094-0.1659266502250.0276675426152-0.0129366621592-1.68538116186-0.2027767084540.221586995914-0.00600515397558-0.00581001553360.1525058736440.0603715496130.225938038413-30.302374224411.363612684135.475731352
175.23857277276-2.218172510111.278973940755.12544257652.47773872682.589800163630.906079977326-0.0537776848271-0.373362362515-1.20192159781-0.124052299557-0.628768880608-0.6116628004910.7510024702430.1381237174270.3172255778280.02469918781630.04746412899430.1104700250780.03815691564210.16175557057-14.34054069564.235230401523.8174667322
183.45544577218-1.3754054333-0.8000447985263.940264496111.77617041853.798711802450.0296822964272-0.2266094966080.581953227436-0.1785588408580.383598168871-1.53705659354-0.2937966248570.725897419042-0.1380272919790.130773170544-0.004837713296830.07591725391980.2208449236510.03137887769360.229168578713-11.9055343441-1.5454945690527.2380824264
192.52295206521-1.67411256649-0.5364863307992.8833820647-0.3331145974912.423793347830.0993505469185-0.3959691162160.353160204837-0.09220932420850.301723488062-0.427690111444-0.5256199365320.386008915345-0.1352282331090.3061598894940.02064305523780.05823900128480.179354325522-0.001276001324990.231444409798-25.899950445814.371240091437.0820985602
202.67411193903-0.261348649225-0.2032410806574.36146245660.3081616768073.04033768580.197963192863-0.214811652087-0.08633240265430.300570651437-0.5870306144520.06141237119960.108482861473-0.4441496245220.03039221270710.1594455688260.01538979389190.04943317919350.1793880665050.01459133984630.167322565105-22.7267538316-1.14446068735.1083273616
217.44967386354-4.34459970503-1.719103154613.063951768192.611552898735.171630955820.3306618252870.502450603124-0.916235116646-0.532973214738-0.5442278017830.627775913276-0.732875232879-0.4390054170730.07448674551040.304805130685-0.07764169894980.07302181574820.271857296099-0.00938667857820.219875656532-27.1449652835-11.012579229530.7803165004
221.63735036185-0.556508910544-0.9420716517094.636850302821.873692226863.18829084209-0.01688467571570.006933914841980.01163133284020.05826474350060.115088468267-0.09592279774430.1459945814150.248413017422-0.07238375775770.1250647325030.01282844306320.001089963745790.1602940708430.03128842395650.161692986833-17.9793296307-1.2440642463833.4494355908
232.90097123094-2.17685991206-0.9392979217753.646725083491.912177673334.637088052370.09948534941150.379032599407-0.0540881964501-0.318889242654-0.2436934963660.0979371047992-0.143069351375-0.1793683429750.002789041610390.157617333658-0.06133888321290.01944525792970.06602331852880.05670606180390.127071659613-22.81936762670.86906623176829.5371000087
242.939975935040.51112494901-1.564493645082.92806267563-2.206388444247.939398178640.3551310487030.01497546343910.014322166961-0.288221246556-0.343217438976-0.378239211247-0.06324478814981.186920454780.07809124827350.2375726926980.0663631134820.0446321450570.183791868394-0.0004412450298330.248920132841-6.31832300638-22.666101688432.481992988
251.40656097141-2.035029482810.6567462488838.25281686976-0.90947220760.758143048769-0.138412656097-0.317597553451-0.232343517798-0.2498559306360.2855783585920.4184827931191.08931010739-0.397784275829-0.0604341607220.310725906378-0.06650671150870.002681869352190.159506524270.002815187508630.170817607128-12.93689355-36.911715912345.2793976212
262.416322367830.828387355580.8196074465111.33574527862-0.7692255159355.031840227170.3224229055080.0463996477420.2767894940890.5772439835850.07716856463410.430024905663-0.3699787995830.0901997140689-0.2124922678310.2528208392460.03314491568290.04750220625450.154171674784-0.04153746995140.15839516374-11.7385944093-20.273041367530.7481968472
272.18661670949-1.69979137204-0.5332629229595.06718729724-0.2304599703191.881751400260.4270634355790.152678437261-0.257374305957-0.424180641046-0.3557780559880.3421949646640.103569055726-0.138980258063-0.06074156119130.250187665737-0.0149582836085-0.02953885399060.203349067709-0.02682867065310.136240347045-8.87496052083-37.06133686532.4090321802
282.50096460686-1.188330192451.786633951134.79289566475-1.177610370443.343852474670.0690978145532-0.00854798098866-0.208805356087-0.0746986543926-0.03381885968220.04955999098670.434303556996-0.03170963465580.004653045797350.202896115045-0.02838797781860.009197496179990.113263939571-0.03932447733040.161447180394-9.36578833016-39.893048604638.5446945241
292.07236327542-0.2775881771571.09514344254.50231509881-4.013044197475.7559889867-0.1213681908470.4256470673740.2905350214770.514453951571-0.606149838889-0.767777962458-0.6164055162291.161526438790.03472217272760.3858965379890.02352750398120.02274963605060.158514313332-0.09715917200690.191474778405-4.9388908468-29.02342159831.6698069691
304.696352836950.468918662164-3.331914706783.62948570445-0.26771366838.478658404260.0851636640577-0.353153599228-0.6122705817371.01161130385-0.261253658298-0.02500259319611.546674154870.08779857302870.3089787892080.445416707592-0.01384532909640.003430902414320.300747209899-0.04527453333680.22972986293-9.5572933287-45.169253629951.6863159565
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 12 )AA2 - 121 - 11
22chain 'A' and (resid 13 through 17 )AA13 - 1712 - 16
33chain 'A' and (resid 18 through 38 )AA18 - 3817 - 37
44chain 'A' and (resid 39 through 52 )AA39 - 5238 - 51
55chain 'A' and (resid 53 through 82 )AA53 - 8252 - 81
66chain 'A' and (resid 83 through 92 )AA83 - 9282 - 91
77chain 'A' and (resid 93 through 102 )AA93 - 10292 - 101
88chain 'B' and (resid 4 through 12 )BB4 - 121 - 9
99chain 'B' and (resid 13 through 25 )BB13 - 2510 - 22
1010chain 'B' and (resid 26 through 38 )BB26 - 3823 - 35
1111chain 'B' and (resid 39 through 62 )BB39 - 6236 - 59
1212chain 'B' and (resid 63 through 67 )BB63 - 6760 - 64
1313chain 'B' and (resid 68 through 82 )BB68 - 8265 - 79
1414chain 'B' and (resid 83 through 92 )BB83 - 9280 - 89
1515chain 'B' and (resid 93 through 103 )BB93 - 10390 - 100
1616chain 'C' and (resid 2 through 12 )CC2 - 121 - 11
1717chain 'C' and (resid 13 through 17 )CC13 - 1712 - 16
1818chain 'C' and (resid 18 through 25 )CC18 - 2517 - 24
1919chain 'C' and (resid 26 through 38 )CC26 - 3825 - 37
2020chain 'C' and (resid 39 through 46 )CC39 - 4638 - 45
2121chain 'C' and (resid 47 through 52 )CC47 - 5246 - 51
2222chain 'C' and (resid 53 through 82 )CC53 - 8252 - 81
2323chain 'C' and (resid 83 through 103 )CC83 - 10382 - 102
2424chain 'D' and (resid 4 through 12 )DD4 - 121 - 9
2525chain 'D' and (resid 13 through 25 )DD13 - 2510 - 22
2626chain 'D' and (resid 26 through 38 )DD26 - 3823 - 35
2727chain 'D' and (resid 39 through 62 )DD39 - 6236 - 59
2828chain 'D' and (resid 63 through 82 )DD63 - 8260 - 79
2929chain 'D' and (resid 83 through 97 )DD83 - 9780 - 94
3030chain 'D' and (resid 98 through 103 )DD98 - 10395 - 100

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