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- PDB-8trf: Crystal structure of SM0281, an alpha/beta hydrolase from Sinorhi... -

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Basic information

Entry
Database: PDB / ID: 8trf
TitleCrystal structure of SM0281, an alpha/beta hydrolase from Sinorhizobium meliloti
ComponentsAB hydrolase-1 domain-containing protein
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homologymycophenolic acid acyl-glucuronide esterase / : / palmitoyl[protein] hydrolase / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Chem-PE3 / Palmitoyl-protein thioesterase ABHD10, mitochondrial
Function and homology information
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsStogios, P.J. / Evdokimova, E. / Lemak, S. / Edwards, E. / Yakunin, A. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other governmentGenome Canada Open Plastics Canada
CitationJournal: To Be Published
Title: Crystal structure of SM0281, an alpha/beta hydrolase from Sinorhizobium meliloti
Authors: Lemak, S.
History
DepositionAug 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AB hydrolase-1 domain-containing protein
B: AB hydrolase-1 domain-containing protein
C: AB hydrolase-1 domain-containing protein
D: AB hydrolase-1 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,02815
Polymers122,3594
Non-polymers3,67011
Water7,008389
1
B: AB hydrolase-1 domain-containing protein
C: AB hydrolase-1 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6687
Polymers61,1792
Non-polymers1,4895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-32 kcal/mol
Surface area21950 Å2
MethodPISA
2
A: AB hydrolase-1 domain-containing protein
hetero molecules

D: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)63,3608
Polymers61,1792
Non-polymers2,1816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area3570 Å2
ΔGint-22 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.528, 130.173, 136.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
AB hydrolase-1 domain-containing protein


Mass: 30589.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc00361 / Plasmid: p15Tv-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92KS5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 30% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.46→30 Å / Num. obs: 55702 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 45.09 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.042 / Net I/σ(I): 15
Reflection shellResolution: 2.46→2.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2692 / CC1/2: 0.669 / Rpim(I) all: 0.453 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→29.69 Å / SU ML: 0.2488 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 23.6441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1775 3.57 %RANDOM
Rwork0.198 47878 --
obs0.1997 49653 88.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.82 Å2
Refinement stepCycle: LAST / Resolution: 2.46→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7772 0 107 389 8268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00387997
X-RAY DIFFRACTIONf_angle_d0.752410761
X-RAY DIFFRACTIONf_chiral_restr0.0461201
X-RAY DIFFRACTIONf_plane_restr0.00471393
X-RAY DIFFRACTIONf_dihedral_angle_d16.8963043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.530.32911150.26652978X-RAY DIFFRACTION72.5
2.53-2.60.28711140.23433365X-RAY DIFFRACTION82.21
2.6-2.680.27171420.23013431X-RAY DIFFRACTION83.81
2.68-2.780.29271270.22673468X-RAY DIFFRACTION84.47
2.78-2.890.28531360.21963533X-RAY DIFFRACTION86.27
2.89-3.020.30761450.23413595X-RAY DIFFRACTION87.63
3.02-3.180.2691250.21063703X-RAY DIFFRACTION89.19
3.18-3.380.21951320.19853795X-RAY DIFFRACTION92.18
3.38-3.640.22391400.18763802X-RAY DIFFRACTION91.53
3.64-4.010.22491390.16353842X-RAY DIFFRACTION92.56
4.01-4.590.21431500.16074006X-RAY DIFFRACTION95.47
4.59-5.770.22571510.17974096X-RAY DIFFRACTION96.7
5.77-29.690.24481590.234264X-RAY DIFFRACTION97.29
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)
15.721066384462.5353030963-1.637550304638.73206370405-2.696050904028.71162179860.0466971157124-0.7300349219540.4205967988580.722008873281-0.241040296909-0.355388027313-1.066618175640.687835560960.1530725606210.438110434097-0.0232445817859-0.1202516118450.357509174324-0.05052655709980.39609673556518.888073715936.962982481526.7596903722
22.010355758070.704904576447-1.593288315184.06836196673.193263020525.86114037917-0.0883931005197-0.380337609419-0.05434225723670.575460207581-0.137252297145-0.068144546382-0.4223413742450.3743225885030.246768985570.444138811644-0.08183631714520.03379719806130.3720179795750.05052564405040.32320096489712.694856387126.645889637331.6779245802
37.87011223898-1.975233401653.055246988937.95093753474-5.448228476454.181471974430.0430002187787-0.8729678143090.07560589719381.03142401735-0.1726252234810.107164960364-0.6662065140350.1153155895130.145923861840.5179940314820.0607682322841-0.003888632841610.505568932927-0.007849346357680.3483755267969.8657080658727.319577366837.1925608438
43.80401133510.425684902460.8345316345016.26963520221-2.858610770276.0431274415-0.0411781390986-0.1699678768080.02148884704480.24257309767-0.0557753854911-0.411495998223-0.390712963490.1882689313240.1031553007770.1988781344590.00172532225587-0.01143905680440.292009808239-0.03414944595860.23266759863713.114304589428.836775892820.7117533923
51.29453041652-1.940360700632.670499257424.57965048979-3.688970894236.544969652010.2563549340770.014086750441-0.405934524941-0.103512998966-0.1133436375110.05254304484420.5202228984630.121045338454-0.1513380663380.2659286668330.0091869699581-0.005762319374550.3032668410920.05152943855430.3664687058742.9015719994625.1827718912.6967074151
67.9425738994-2.59848996673-5.396396230732.509829484382.255515316953.87809994281-0.15653258093-0.812521110663-0.127761834421.080629691490.24848222871-0.341870131417-0.122236963999-0.637682040057-0.2876165760860.5147076960820.0268263178373-0.002331659675480.5658901385060.03218943236410.448900875261-5.1873121928639.530006063814.0034188757
70.823457259242-0.256585846245-0.0726811373214.47752920133-2.750070852483.42022616386-0.0854721644741-0.153465774624-0.213639626516-0.128327028580.3504312660830.2679225497180.266227349755-0.445546639203-0.2469240847420.31570239795-0.0394033161738-0.05925172786170.3755633959110.05851565823180.3822083564471.5321549327320.526963557715.6414293995
82.667372047820.7345094465830.8532569425387.846360292881.016236370685.26296513582-0.0928404421383-0.477510692723-0.2081312293030.05185861802550.2750115754450.569413570592-0.273258764938-0.596539887909-0.0912774834550.295441898541-0.03863771464470.08052661964940.5107146302520.1908146429910.429510654342-2.9344404113917.552082236126.8930607661
97.247414151422.837516694720.1937172222775.61051517013-2.269846129099.344723314350.0576324322805-0.45242774856-1.372622132220.595825944202-0.1208118514550.132957256332-0.418968053228-0.3701646146450.0747774315160.499620113235-0.0427674607583-0.009152404709740.4969256519540.1067802617590.3460123083233.1638174276117.615452473836.5794131626
107.14365202916-4.34115993689-5.02295162617.93499030365.182121244554.654687272760.3062808747230.2623536012280.709441748533-0.8128694092630.169212103647-0.634261719786-0.325100556433-0.0844100481394-0.5197245569090.449512747557-0.0597628707032-0.02840017313960.4847421016540.04383758365330.380234687639-4.216092642560.8150485431-3.09115484876
113.13915931704-1.38380098473-0.95175942272.90709341856-1.276502982831.71248879846-0.158204596143-0.2453881379410.7408238966720.0268709469285-0.00796045785863-0.223997976573-0.5299558229560.1416914216610.1771031125250.3290162032450.01822885751580.01092878287750.292254644152-0.02988024730650.378924484284-10.060192927664.90350188157.65005770505
122.63357354356-0.0686792334144-1.568197381394.625869293761.801349866223.73148724268-0.009780638107720.1905153882660.176995205336-0.2702782442520.163822111254-0.118429029343-0.227322726937-0.0897144239075-0.120996226310.298192825077-0.0100213721753-0.02912678144580.3243746467320.08693414695620.276710992332-13.08113444962.59947154822.1747843737
136.51773553821-0.870949191142-2.635179041565.09057359583-3.346932272358.56059256710.229343002631-0.4271463157120.4608837574250.105147459899-0.0336815295034-0.728389611196-0.2643154492791.04816032158-0.1639745270710.2023124141970.02421891809530.06592281481660.4646304625440.03879072209210.345022979607-4.1489970875155.01556340394.84465026481
148.241964101391.900376684292.553105967262.211551109242.815031469357.46766463816-0.320328682874-0.6784453658460.0673191108509-0.112500976693-0.00325890863786-0.0774970441543-0.1276143153230.2182791241670.295068716330.2364905361570.00161658177665-0.01200931354850.243287525486-0.002744753816490.282311316486-10.532040725154.869726606512.534264548
150.9127998003692.029365724271.344733106186.219290504952.351338695773.483487093570.331486135976-0.1036216033780.01853029689370.508711946721-0.0982605370442-0.2376025673270.1195136922920.159166742069-0.2462568321480.237865266506-0.0120999787295-3.81039662601E-50.33595622897-0.02409389123460.33292510398-17.184432349949.036583111512.215869341
169.35328889787-3.983912514171.076364203632.03702270353-0.2754673699388.602472712150.157359309414-0.04910907098160.02737116703290.288971906536-0.173176156655-0.0907341643919-0.7506594356680.103928633531-0.03660259931720.311674842334-0.02976922222040.001462330598520.290924664036-0.03319279986890.266323847607-26.71806619441.4454196593-5.15541452
178.910375618222.483798752723.922266682661.759248124452.161326121097.02637565784-0.0361936975290.08713229349-0.2061178418680.283619220478-0.156242828534-0.3149219209870.7103272003720.1475452190560.2497116043270.32292610731-0.007354740042540.0972094484640.3257372769620.1014548752540.379288509037-16.156357912740.63518089752.05107290391
183.50149146870.102376871829-0.6692617108495.486903895012.512245855312.57851787093-0.103849029556-0.266103802278-0.1831375783160.254073915528-0.05462973064020.2213777872680.3519580594150.01669761084990.1595623831520.341109998918-0.01612322671580.04242415608840.3786648963910.0228265738510.215557545539-21.182987107450.771812234218.2137806253
195.20740496417-1.42644551298-1.161348148158.95662537404-1.351496617114.73819347653-0.01421594962180.310161547898-0.0838670981061-0.2299374801380.06580712300310.275243093316-0.217319863112-0.09505610838-0.05822164812050.2179726799030.002955417383050.04144412574620.419130743966-0.1006358426510.269745030007-24.976108635558.643193398817.8123340281
208.248480646552.927150487340.5536889229067.048848048291.756845169457.069173838510.0881422106916-0.552555141449-0.2154467777330.175653966218-0.04149427106920.470472682565-0.344378353042-0.03023714818930.1566236536080.4539000473980.03634019287620.08714929342950.263515825706-0.07601404085040.328955622913-19.346479115568.597619413517.5236028466
213.276591734812.30018267893-3.060661697331.73776168055-1.95306035075.749804152550.334952720457-0.5987958349760.3727097250540.380748375795-0.127977024720.0132669108408-0.4294229505450.270765211631-0.1852465179690.36178398064-0.06123861960960.01618577961870.571523747477-0.1413443262970.470300077794-35.284445969272.195285221146.0009118086
225.95398122326-2.258084877450.9641167913668.872964620861.791995998782.363541868930.169986130887-0.5041536782650.1986733499260.35104706917-0.566179540312-0.03397885188230.131043101995-0.314354207930.3543513431310.282771120232-0.08147063048570.05077295875920.611262551111-0.1347582027840.379494543649-43.456449988365.458390846247.4542818945
232.58852864972.6640104875-0.7493843656538.53958745604-3.600761540986.25403995104-0.043352799359-0.00297365836868-0.398633177221-0.07604064999720.001971624987830.2414545945870.475531520678-0.4545016665620.006073033967050.304078494144-0.05500674488930.09530947926170.482032950383-0.140910471730.491209021315-41.228769545155.79250697237.7903058274
248.33144313771-6.142959441515.121091392779.45793603248-5.502372656814.34603956628-0.365994310088-0.232592029431-0.3584258831610.9547817994020.0919783936626-0.271497225029-0.305464983189-0.1868490137420.1927047737480.582235535264-0.1165475947160.1230382681440.674839814898-0.07291734436480.586751881362-41.769835398147.535994131548.8942538946
250.0447956397995-0.376902476286-0.7361133290287.848716993351.764966391574.28493579639-0.0356098790360.686571209225-0.6035794294-0.826798357972-0.3794921423171.382982058280.460862289593-1.219255600510.3045974901970.443656426073-0.104277641605-0.08604717147590.705208265969-0.1861659795480.810481563133-45.815521100658.987670626428.309098051
264.10276047399-1.81305185084-0.772916322699.24314957323-3.507464700714.51849163217-0.0907000248268-0.141797815709-0.2881494920220.235956198112-0.1438297033280.1692200022560.232001693617-0.001198379672080.2071752370060.343188445322-0.01955722891090.05144971995330.458485320941-0.03993853348890.297715564999-31.837551801154.442740664529.6526050079
272.881721037780.929335574104-0.5045114592458.03634078249-0.2818542192297.15117128730.101281485499-0.00955198742192-0.1007637463630.102471690717-0.146340673091-0.08542346016550.01778073640320.249214618330.02906673445730.164271661698-0.007469254352090.07615911399640.325930384276-0.09744701145440.28339250693-26.860149949664.286940489530.1581631226
284.04500700096-1.702792060070.3823112047945.6402412738-0.948878477482.500270252170.1817197061220.482629821289-0.810419087669-0.22933326647-0.4145389930750.06027705968160.2994630321510.2281255058480.1791414911770.5203602549470.0970226379949-0.07688500194340.676280917819-0.2799780561180.69014039036914.242546850455.944939263324.5684893194
297.97399672540.03680231920424.083726928037.61091529677-2.91032757883.35852266141-0.0317852517302-0.38771836478-1.156001444940.06578945207640.136722214139-0.7120576148251.02613204107-0.124196142442-0.03624337790520.5145463333430.0272948410892-0.01175209455110.54963264903-0.1210559378710.75185011941621.867847069549.261506936235.4223221512
309.687990737184.07968793860.008682477318075.435889022133.626041276863.83450746370.1195062154821.173927553690.0414747817337-0.3741082827930.396559394294-0.474985223929-0.1690142575251.59917274686-0.5291815981840.500639976580.05143827911990.08620570080940.61868574537-0.1291491480360.74079640191524.39511150460.178404737526.1156866795
314.16249946972-0.9695829865193.059104898584.15211401146-1.015024697164.94641149405-0.12059060265-0.401159977253-0.1056029343220.114857925059-0.1846234351260.003204040778760.122502635556-0.09449707131360.293744890640.3590159474760.03043173717950.02563898159150.593681432249-0.1092486301110.57108279780721.682327977864.128160263340.8048979127
326.729974189654.33331546502-3.579790636024.12326207689-5.585767723389.68563817309-0.033540626526-0.0148224356788-0.9142347390690.424264736467-0.1800221668810.1385179061950.0994824844466-0.537023306210.169567884990.519919207358-0.03761147206550.05803408563390.701673349415-0.08419455071040.79602501539325.301917975554.012876294548.1303327459
330.844875067196-1.569589514570.4961863199592.85435399634-0.1879248505936.88861033164-0.01813957610150.148509716224-0.08294801665990.5806650558420.121483857916-0.547825083365-0.2965462053930.603557112337-0.06276738264150.4317491140320.00130139521821-0.1098309069420.572462759743-0.1904112471980.57954711571615.206864632971.358696597940.598427194
346.44053300942-3.454301575751.920839718262.10508105925-0.02510801488169.53240560190.0703377684792-0.2401265537390.4857145316780.1109698757420.117577615844-0.772265386033-0.1271473414571.01127301094-0.1560161077790.4056231591380.0829675096656-0.03165939792210.579105111535-0.2468571192560.63645382707413.374665710476.156662779541.3719536177
352.32582577204-1.87870333017-1.807026945953.17948926895-1.002817434177.273230493760.1912343969650.0377482297311-0.1609287000860.0331175051173-0.0451365190985-0.2108574871150.05087083998330.723082426896-0.1170866778180.3556652507460.0386066637637-0.129944871230.633510663084-0.2457274050480.6577410090313.1478974334667.82850640233.6245020189
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 29 )AA7 - 291 - 23
22chain 'A' and (resid 30 through 59 )AA30 - 5924 - 45
33chain 'A' and (resid 60 through 79 )AA60 - 7946 - 65
44chain 'A' and (resid 80 through 133 )AA80 - 13366 - 119
55chain 'A' and (resid 134 through 179 )AA134 - 179120 - 157
66chain 'A' and (resid 180 through 193 )AA180 - 193158 - 171
77chain 'A' and (resid 194 through 242 )AA194 - 242172 - 220
88chain 'A' and (resid 243 through 262 )AA243 - 262221 - 240
99chain 'A' and (resid 263 through 280 )AA263 - 280241 - 258
1010chain 'B' and (resid 7 through 29 )BH7 - 291 - 23
1111chain 'B' and (resid 30 through 59 )BH30 - 5924 - 45
1212chain 'B' and (resid 60 through 95 )BH60 - 9546 - 81
1313chain 'B' and (resid 96 through 113 )BH96 - 11382 - 99
1414chain 'B' and (resid 114 through 133 )BH114 - 133100 - 119
1515chain 'B' and (resid 134 through 170 )BH134 - 170120 - 146
1616chain 'B' and (resid 171 through 193 )BH171 - 193147 - 169
1717chain 'B' and (resid 194 through 207 )BH194 - 207170 - 183
1818chain 'B' and (resid 208 through 242 )BH208 - 242184 - 218
1919chain 'B' and (resid 243 through 262 )BH243 - 262219 - 238
2020chain 'B' and (resid 263 through 280 )BH263 - 280239 - 256
2121chain 'C' and (resid 7 through 79 )CL7 - 791 - 61
2222chain 'C' and (resid 80 through 114 )CL80 - 11462 - 96
2323chain 'C' and (resid 115 through 179 )CL115 - 17997 - 151
2424chain 'C' and (resid 180 through 206 )CL180 - 206152 - 174
2525chain 'C' and (resid 207 through 218 )CL207 - 218175 - 186
2626chain 'C' and (resid 219 through 242 )CL219 - 242187 - 210
2727chain 'C' and (resid 243 through 280 )CL243 - 280211 - 248
2828chain 'D' and (resid 6 through 79 )DN6 - 791 - 62
2929chain 'D' and (resid 80 through 95 )DN80 - 9563 - 78
3030chain 'D' and (resid 96 through 114 )DN96 - 11479 - 97
3131chain 'D' and (resid 115 through 179 )DN115 - 17998 - 152
3232chain 'D' and (resid 180 through 207 )DN180 - 207153 - 174
3333chain 'D' and (resid 208 through 232 )DN208 - 232175 - 199
3434chain 'D' and (resid 233 through 253 )DN233 - 253200 - 220
3535chain 'D' and (resid 254 through 280 )DN254 - 280221 - 247

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