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- PDB-4tza: TGP, an extremely thermostable green fluorescent protein created ... -

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Basic information

Entry
Database: PDB / ID: 4tza
TitleTGP, an extremely thermostable green fluorescent protein created by structure-guided surface engineering
ComponentsFluorescent Protein
KeywordsFLUORESCENT PROTEIN / thermostable / engineered
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsClose, D.W. / Bradbury, A.R.M.
CitationJournal: Proteins / Year: 2015
Title: Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering.
Authors: Close, D.W. / Paul, C.D. / Langan, P.S. / Wilce, M.C. / Traore, D.A. / Halfmann, R. / Rocha, R.C. / Waldo, G.S. / Payne, R.J. / Rucker, J.B. / Prescott, M. / Bradbury, A.R.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Feb 17, 2016Group: Data collection / Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Fluorescent Protein
A: Fluorescent Protein
B: Fluorescent Protein
D: Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)113,0114
Polymers113,0114
Non-polymers00
Water14,700816
1
C: Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)28,2531
Polymers28,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)28,2531
Polymers28,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)28,2531
Polymers28,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)28,2531
Polymers28,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.1999, 141.22, 69.0897
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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
Fluorescent Protein


Mass: 28252.732 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pETCK3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRQ is the chromophore that folds from the amino acids QYG, which are encoded in the original ...CRQ is the chromophore that folds from the amino acids QYG, which are encoded in the original sequence. MGAHA represents N-terminal residues added when expressed from the plasmid. SGGGSGGGASGKPIPNPLLGLDSTHHHHHH are C-terminal SV5 and His Tags.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG MME 2000, 0.1 M Tris-HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→28.6 Å / Num. obs: 72746 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.7964299494 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
HKL-30001.9_1685data collection
iMOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHENIX(phenix.refine: 1.9_1685)phasing
PHENIX(phenix.refine: 1.9_1685)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.5861694308 Å / SU ML: 0.187768078998 / Cross valid method: FREE R-VALUE / σ(F): 1.33087988092 / Phase error: 21.7324419422
RfactorNum. reflection% reflectionSelection details
Rfree0.200305594674 2047 2.84887200256 %Random
Rwork0.173763175365 69806 --
obs0.174538516473 71853 98.0112125056 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.4435785015 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.5861694308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 0 816 7826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006885517349277209
X-RAY DIFFRACTIONf_angle_d1.234343424359720
X-RAY DIFFRACTIONf_chiral_restr0.0408730419139982
X-RAY DIFFRACTIONf_plane_restr0.00504121062131264
X-RAY DIFFRACTIONf_dihedral_angle_d14.33469043962746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.4357829295631120.432767068473969X-RAY DIFFRACTION84.8088113051
1.9442-1.99280.2499482030011440.2315151577644679X-RAY DIFFRACTION99.6281759967
1.9928-2.04670.2103302967481360.1869418011594699X-RAY DIFFRACTION99.8966942149
2.0467-2.10690.217954550351370.1829595170194669X-RAY DIFFRACTION99.9168399168
2.1069-2.17490.20365569341550.1855034939344664X-RAY DIFFRACTION99.7929177884
2.1749-2.25260.3366166763931110.2967932762244453X-RAY DIFFRACTION94.1224994844
2.2526-2.34270.3069048976911210.2354782522354419X-RAY DIFFRACTION94.0542780195
2.3427-2.44930.2319381708921330.1782712308114727X-RAY DIFFRACTION99.774173681
2.4493-2.57830.1862275748781600.1749194229284699X-RAY DIFFRACTION99.7331691297
2.5783-2.73980.2078550544921420.1665198287194717X-RAY DIFFRACTION99.7741273101
2.7398-2.95110.2143830176881470.1747374974384738X-RAY DIFFRACTION99.7753267974
2.9511-3.24770.2029283064421280.1695350429554763X-RAY DIFFRACTION99.8774760057
3.2477-3.71680.166764965961400.1579256057614771X-RAY DIFFRACTION99.6146044625
3.7168-4.67940.159835001251390.1253340130884835X-RAY DIFFRACTION99.6593868964
4.6794-28.58940.1468965786991420.13536754715004X-RAY DIFFRACTION99.4204018547
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)
10.167617919963-0.1082958789560.05615352410330.0819901439007-0.1762891834640.189593876777-0.0376146959854-0.0716765742172-0.0523358649365-0.0448202466112-0.1259723307450.201500960784-0.0179874695189-0.207791781508-0.003542380968810.10706187719-0.002054629504080.004454409897440.17912419594-0.05320156184840.160365935038-7.17544736681-8.52417454687-27.2268026453
20.1658722149620.07839555092430.05286882775990.0406720415275-0.08032401426310.1075421291570.03386325091120.0803330345352-0.0255953212838-0.0322469296928-0.04951577595980.0615015266998-0.0118916083666-0.094474264951-4.6931825371E-60.148104612950.0155459615242-0.01907954772510.189521735083-0.04378328741490.144880611363-5.59442918668-2.51796025344-30.1416579336
30.2052350681030.02518562611530.03813445482280.02941697906510.02471577718410.01465562636280.01239434480510.190533052954-0.3133362691950.0878404316259-0.07834384772580.150845222477-0.02098894359130.00734638896835-0.0560412872980.2038831344110.02369041981390.01438873296540.204001393904-0.09568012587830.1923352510484.72088077424-18.1262543011-38.344902971
40.03372945059630.02548077934720.02489711958950.03492131188250.03843106928910.08771702034740.01332686827950.0499134197609-0.08277495631170.163151770217-0.010274648477-0.296225008009-0.03554289160170.0799786801036-2.25127457777E-50.131497095968-0.0139227666206-0.02279557912810.1092355032820.01314443889320.128364159437.92615896458-0.140909879822-26.4340100705
50.0408536054512-0.07290976951910.02824270964450.0533467483153-0.07059256995550.111423650573-0.0342911147733-0.17595654461-0.1250664959610.0241036302764-0.0775224131770.110724535783-0.0299969059184-0.0718689332491-0.0005201955721020.135677832037-0.009378123310410.003367108184060.1238123954210.001904637726740.175655902532-1.30378935112-9.77813162628-24.3735522668
60.1336300288620.175758674905-0.1251164871290.1212748698190.0781916577480.024304985875-0.002268031664280.116772957740.0862059592658-0.0208353429669-0.0876065343196-0.0707288890962-0.1159338926780.109378586879-0.0007301541231430.2509172637050.0340478533517-0.01146494837610.177968676665-0.001836821723170.1501426092625.534876671284.71153395025-31.0677328819
70.06588274222370.01933401845930.07629530729940.102380734090.04969058997360.04490114544030.07268551398150.17484452214-0.01889477436360.0185788570929-0.173874584499-0.0648485056945-0.08952533238060.1813010377380.003786397033820.176046288920.01561892094040.01270564412810.1584889717150.02724645335010.09780221981068.232033595471.67001295099-32.9048039231
80.2543673550610.1945498328730.1153694462820.2140584595050.06159666978850.151578019325-0.1032808190470.139050070721-0.171444091638-0.1108296936370.0458054361659-0.0229468193205-0.0379296918152-0.1222009546450.00267331087840.2389671071430.05044979501230.01204776388330.247198365929-0.02670732882380.1971902986364.38449484519-9.41445156697-37.5643991466
90.053739314279-0.08208435544570.0742810177806-0.0176082780238-0.08875007638360.222063435009-0.130345684774-0.0663025782796-0.00605121808961-0.2670511263940.01999105228480.0845239217938-0.0827677523592-0.0208610030335-0.03974427523960.1853838646110.0766172233107-0.03911096919870.277927426966-0.04363333827060.180758576524-5.52699784577-1.323709417-36.4409398939
100.21289604452-0.2173400556740.2050652922620.1720710609-0.1990152271750.1445195980760.00841696795784-0.195690814724-0.05997983122280.00317754996488-0.0003180911969480.1721733289220.11750489679-0.1022786894010.03397162616050.195378079711-0.00868233470774-0.01332961989470.208097656351-0.01053969853560.1524088198166.635608657150.4025224010090.99918528118
110.236081306683-0.1250851523620.1427334391410.078675441909-0.1345641017030.267950899785-0.0138297550004-0.1773461089920.0245162187082-0.0283823488298-0.01812581423110.01699142530540.0174529164596-0.102534366347-0.006304861069530.1954965148230.0238924067589-0.02713446187640.171077230102-0.02648424200510.12998989073413.70718065594.27889765805-0.0792153769332
120.244565865426-0.2914840133920.4062594604570.171150740122-0.2359571467610.4661713962240.05035416828730.08113958663630.505273360166-0.1127465995170.1053384902440.7900012594610.0682970741275-0.1266240163060.1153145662150.1497314931280.0402837311834-0.1355042354290.131800353494-0.121152104537-0.2502450281210.0751667153.42001460971-8.40907893507
130.06924702487460.0828625245093-0.01796163034340.06184228893350.05587912374810.1850548686790.003259285936490.1146055924540.136272676936-0.0592979702634-0.08214674605410.06399647339710.09618861162420.1553995181040.0006264049414130.2001255517740.0279125141925-0.03114638928030.1658688840.02188628534450.19333620636920.28218473949.67700520325-10.1890496172
140.1577013313150.1337515826240.05551889054010.101017365626-0.01071775187860.094582139609-0.1277833015350.0660324838463-0.00796444707617-0.07678831805-0.0490390355750.04601493211540.03969244405950.107907513677-0.01568896613520.213516575840.06903446066010.005018590804720.2220461576170.02858449875150.16715948258119.76358587674.98567765299-12.272921785
150.0714686419088-0.0325645639874-0.03645185520240.06038493948610.04915563509680.194019093589-0.0287818510255-0.1096952721680.2123883161240.08161988123280.0595366372781-0.06373531559140.0397707308826-0.002374285776490.001589138821030.1448932661710.0337160925172-0.03388772443520.113068162173-0.00768459370560.19994007830715.336709496612.8656683025-2.25518255236
160.333914817703-0.12517021558-0.03730749307960.05442644920370.01048215199690.0403258331468-0.0371296676123-0.1437344479620.0143244959282-0.07798439286690.112877325435-0.007024017352850.08067052398640.04864941493720.04137503819230.2199901631030.0103163267182-0.04209783381810.1784858562050.02599215128770.13522621655918.51499042650.7258680205341.6315204823
170.2373860125170.08750643127350.08357879507870.132484241877-0.03968933330380.122290130115-0.109572367125-0.0548240719016-0.0850123887401-0.285887643757-0.1516362573380.03077189673410.09476098478190.0923190332856-0.0948370987620.3658064132670.04200898380950.0493824807180.1084081507490.05645086942560.16915852886518.0244642231-42.6065880909-19.3617204366
180.0535986997052-0.003587005285010.0250876164762-0.004410495301910.009186923290080.0225794397577-0.01953323696650.00962206129399-0.0315698695686-0.1073922602490.01143862686510.05536536162970.0175196400601-0.0228410028945-1.68558992643E-50.2745779621030.00589211788578-0.00297303627290.1614860088340.037665691580.24470093669611.7004666521-44.4358632506-15.2081597998
190.1788017571480.01072617959760.1963586134730.503218722765-0.415020833950.528859670548-0.0886856026834-0.092881770648-0.106728365448-0.215366678345-0.159911755353-0.06394408268360.1541318418630.173253881242-0.5839287348530.2213055215680.02491534565750.03196553239840.1458286662330.08295224738540.23367761175419.8934021487-36.2823921691-13.8553141261
200.5895946163180.07593837938820.330768315840.1862410034760.00979144280140.180293921229-0.0662281083483-0.5325436727340.0145586543378-0.226116332519-0.248543685272-0.1887524340.186309358702-0.0397277380229-0.09883603345720.3199068260420.08276638265740.127262774666-0.07715167539420.1497457430890.25704334424721.1246268731-44.5467114724-14.0237044801
210.01446553816750.0201151529939-0.004026057095070.01654480717310.003148388820610.02022571141390.0424390897325-0.1229317250450.127426169024-0.0882743557122-0.03565965731640.04758284207010.139188275916-0.041239105515-3.15273630713E-60.1788200295430.006385222526640.05624022786730.2658346491210.04141102411410.2441515853816.61076262879-38.10165677894.76003274723
220.2370599160770.105194216902-0.01497632740570.2750476219480.09940984842030.359897296741-0.115745186833-0.1359863165020.01429659379530.0212139702639-0.0885635113228-0.0715781516312-0.1443016641820.135434633403-0.09607225608560.2247242344820.0004767775935650.0180056867310.2124801073190.1035506535210.35164653546722.5769244261-29.0755041361-5.90427078494
230.02422526309160.078821531133-0.02745142771580.185981938318-0.1761809525530.08498550505530.0293825577263-0.133509853370.08106479834150.106198307677-0.183490516846-0.119358895494-0.04780504001160.01645963494091.68154350765E-50.2720820919880.02195173439140.01563420149790.2617166590910.01209368401330.27137679043519.2444559321-31.7658873603-2.76442872503
240.007288267079240.0112713812792-0.0440508416790.119110213924-0.03721665225970.02547389034850.0436963720053-0.00682089985913-0.083976470651-0.232728725944-0.0350261055857-0.029476410063-0.108576238990.07378689929671.21645018194E-50.2328954002520.00874137124510.03399450647770.2329937630030.07822057595120.38247877866224.5544827397-30.9027818293-15.3580674155
250.0822485262036-0.1733923447180.04946187212310.117448558436-0.089930119790.0292814161949-0.01010312846190.07931468051290.0438191266414-0.07163377518850.01769729186070.0327660622657-0.00204844662055-0.0888546162373-9.30506783191E-60.247272058257-0.00595585978167-0.02200375951650.1686946806440.07051681993720.27910470200711.6112091382-32.4505230787-15.330303545
260.3255418008980.06346104964120.1342964376570.221081304030.03354279460380.4811631757030.112534053609-0.05876447406380.0666384745433-0.0674562731040.0771924749737-0.132938877775-0.145511369954-0.08678044528260.2139343261790.1771781983670.08154908015060.0796921811590.2489619870520.08538235949680.244390746516-25.0770875218-7.24656916636-7.3288547271
270.267377573563-0.0473906504801-0.2484646407760.495063412710.1602575479940.4114788717630.140300370617-0.0114357897338-0.136240487522-0.152863644218-0.00257251248653-0.236376793328-0.110759794461-0.1959877828570.06244762270730.1563230698890.06042710822550.06759788391290.236081660060.0724697814970.218698134881-24.9756172778-14.0851964288-13.289293844
280.6909202912040.1620090257620.09887985967240.2860073998550.24224793460.2202025275510.2961365830160.0471389328381-0.2192969689630.256678119238-0.186053303579-0.230012588089-0.201814047932-0.2421197744770.1055590700830.1200343074120.1088546327580.07314133695030.2918807054360.07801806991960.226433032085-24.0152666748-15.8308468813-5.04991622355
290.0510839069442-0.0803880821146-0.0317359477780.289779587021-0.09901638333090.1500857920520.204443210036-0.297126944429-0.129535517718-0.557548966843-0.154715663719-0.3976071198060.0476691577706-0.361814574547-0.004466447627120.2105916769710.004332506767260.03822402639830.3440205243910.02876243997560.381931165759-21.0706210454-23.4503285737-16.7794754793
300.006714927838930.017498275995-0.006392539399230.0706860710864-0.01899753136280.132828318697-0.03105515320750.04200087500510.0221153767057-0.1150626022970.0781820325449-0.2511749440290.0490160155421-0.144405926232-1.40772415939E-60.2316815549180.04512245685990.07645329242910.2738181165910.03522625714780.428714682106-19.5182889732-24.7107138962-13.4012821561
310.02670189907040.000850938126466-0.05013036508760.133058556783-0.1829136349370.1551763066510.0703863221833-0.03982852413720.0474733584586-0.332078300243-0.0798334999912-0.201441194308-0.191023936088-0.2559949762660.001115164141020.2162135787520.05854649274470.06140742063240.336369954624-0.009969355840080.307726843429-27.188182245-15.7689105262-20.2154221016
320.1057705161160.0766904619518-0.08113450673680.104996618222-0.04942096617370.1126567010070.0971883899116-0.1029597090540.0736619919748-0.269126513757-0.252034561585-0.24738385979-0.00103394587264-0.09651488786660.009804283114910.168301868965-0.02418082807540.124895723380.2663719072990.005882783595360.417055399224-16.6214064385-10.5206561098-14.8813640035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resseq 2:32)
2X-RAY DIFFRACTION2chain 'C' and (resseq 33:66)
3X-RAY DIFFRACTION3chain 'C' and (resseq 67:86)
4X-RAY DIFFRACTION4chain 'C' and (resseq 87:99)
5X-RAY DIFFRACTION5chain 'C' and (resseq 100:123)
6X-RAY DIFFRACTION6chain 'C' and (resseq 124:151)
7X-RAY DIFFRACTION7chain 'C' and (resseq 152:179)
8X-RAY DIFFRACTION8chain 'C' and (resseq 180:200)
9X-RAY DIFFRACTION9chain 'C' and (resseq 201:217)
10X-RAY DIFFRACTION10chain 'A' and (resseq 2:32)
11X-RAY DIFFRACTION11chain 'A' and (resseq 33:77)
12X-RAY DIFFRACTION12chain 'A' and (resseq 78:135)
13X-RAY DIFFRACTION13chain 'A' and (resseq 136:163)
14X-RAY DIFFRACTION14chain 'A' and (resseq 164:179)
15X-RAY DIFFRACTION15chain 'A' and (resseq 180:200)
16X-RAY DIFFRACTION16chain 'A' and (resseq 201:217)
17X-RAY DIFFRACTION17chain 'B' and (resseq 2:20)
18X-RAY DIFFRACTION18chain 'B' and (resseq 21:32)
19X-RAY DIFFRACTION19chain 'B' and (resseq 33:99)
20X-RAY DIFFRACTION20chain 'B' and (resseq 100:123)
21X-RAY DIFFRACTION21chain 'B' and (resseq 124:135)
22X-RAY DIFFRACTION22chain 'B' and (resseq 136:163)
23X-RAY DIFFRACTION23chain 'B' and (resseq 164:179)
24X-RAY DIFFRACTION24chain 'B' and (resseq 180:200)
25X-RAY DIFFRACTION25chain 'B' and (resseq 201:217)
26X-RAY DIFFRACTION26chain 'D' and (resseq 2:32)
27X-RAY DIFFRACTION27chain 'D' and (resseq 33:99)
28X-RAY DIFFRACTION28chain 'D' and (resseq 100:133)
29X-RAY DIFFRACTION29chain 'D' and (resseq 134:163)
30X-RAY DIFFRACTION30chain 'D' and (resseq 164:179)
31X-RAY DIFFRACTION31chain 'D' and (resseq 180:200)
32X-RAY DIFFRACTION32chain 'D' and (resseq 201:217)

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