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- PDB-7vn8: Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vn8
TitleCrystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning GTCACGTGAC
Components
  • DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
  • Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
KeywordsTRANSCRIPTION / Transcription factor-DNA complex
Function / homology
Function and homology information


plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / DNA-binding transcription factor activity ...plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol
Similarity search - Function
BZR family / BES1/BZR1 plant transcription factor, N-terminal / BES1/BZR1 plant transcription factor, N-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
alpha-maltose / DNA / DNA (> 10) / Maltodextrin-binding protein / Protein BRASSINAZOLE-RESISTANT 1
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
Arabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsNosaki, S. / Tanokura, M. / Miyakawa, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05835, 19H04855, 19K23658, 21H02114 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101077 Japan
CitationJournal: Nat.Plants / Year: 2022
Title: Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout.
Authors: Nosaki, S. / Mitsuda, N. / Sakamoto, S. / Kusubayashi, K. / Yamagami, A. / Xu, Y. / Bui, T.B.C. / Terada, T. / Miura, K. / Nakano, T. / Tanokura, M. / Miyakawa, T.
History
DepositionOct 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,10323
Polymers212,0518
Non-polymers2,05215
Water4,161231
1
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,14513
Polymers106,0264
Non-polymers1,1199
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-7 kcal/mol
Surface area41390 Å2
MethodPISA
2
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,95910
Polymers106,0264
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-11 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.402, 94.470, 112.941
Angle α, β, γ (deg.)90.000, 100.650, 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
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 / Protein BIN2 SUBSTRATE 2


Mass: 48419.836 Da / Num. of mol.: 4 / Mutation: D82A,K83A,E172A,N173A,K239A,E359A,K362A,D363A
Source method: isolated from a genetically manipulated source
Details: The fused Maltose binding protein is derived from Escherichia coli O157:H7
Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) Arabidopsis thaliana (thale cress)
Strain: FS14 / Gene: malE, JW3994, BZR1, BIS2, At1g75080, F9E10_7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P1LXE0, UniProt: Q8S307
#2: DNA chain
DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*AP*AP*A)-3')


Mass: 4593.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM sodium cacodylate pH 6.5, 200 mM potassium chloride, 10 mM magnesium chloride and 10% (w/v) polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→47.85 Å / Num. obs: 146131 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.9
Reflection shellResolution: 1.98→2.01 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7248 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZD4
Resolution: 2.04→37.01 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2405 6663 5.03 %
Rwork0.2135 125796 -
obs0.2149 132459 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.63 Å2
Refinement stepCycle: LAST / Resolution: 2.04→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13592 1220 136 231 15179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007615405
X-RAY DIFFRACTIONf_angle_d0.710721138
X-RAY DIFFRACTIONf_chiral_restr0.05842306
X-RAY DIFFRACTIONf_plane_restr0.00362526
X-RAY DIFFRACTIONf_dihedral_angle_d24.20495759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.070.36771700.30274198X-RAY DIFFRACTION99.59
2.07-2.090.35792300.29174216X-RAY DIFFRACTION99.42
2.09-2.120.29932150.28564178X-RAY DIFFRACTION99.66
2.12-2.140.3222420.26494202X-RAY DIFFRACTION99.49
2.14-2.170.31142220.27234185X-RAY DIFFRACTION99.66
2.17-2.20.31582020.25834198X-RAY DIFFRACTION99.68
2.2-2.230.282360.25824171X-RAY DIFFRACTION99.8
2.23-2.270.29792400.26294226X-RAY DIFFRACTION99.71
2.27-2.30.31772270.26354190X-RAY DIFFRACTION99.8
2.3-2.340.29632210.24814183X-RAY DIFFRACTION99.66
2.34-2.380.2912130.25144216X-RAY DIFFRACTION99.68
2.38-2.420.28392400.24914182X-RAY DIFFRACTION99.8
2.42-2.470.26462070.24764227X-RAY DIFFRACTION99.71
2.47-2.520.29522210.24434171X-RAY DIFFRACTION99.7
2.52-2.580.25882470.24554199X-RAY DIFFRACTION99.62
2.58-2.640.28852240.23924231X-RAY DIFFRACTION99.84
2.64-2.70.26892040.24474215X-RAY DIFFRACTION99.37
2.7-2.780.29912190.24094213X-RAY DIFFRACTION99.46
2.78-2.860.29152340.25344173X-RAY DIFFRACTION99.41
2.86-2.950.26782270.25044202X-RAY DIFFRACTION99.39
2.95-3.050.26812360.24084168X-RAY DIFFRACTION99.21
3.05-3.180.27012320.24234185X-RAY DIFFRACTION99.06
3.18-3.320.2572010.22464194X-RAY DIFFRACTION98.48
3.32-3.50.24242200.21184187X-RAY DIFFRACTION98.61
3.5-3.710.21572190.20814160X-RAY DIFFRACTION98.54
3.71-40.22882320.18744163X-RAY DIFFRACTION98.37
4-4.40.19012150.16584183X-RAY DIFFRACTION98.08
4.4-5.040.18092160.15484204X-RAY DIFFRACTION98.62
5.04-6.340.21822250.17454228X-RAY DIFFRACTION98.21
6.34-37.010.1372260.15714148X-RAY DIFFRACTION95.27
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)
12.305361066761.13546150580.5911068181742.28825664547-0.2691040225112.059994562970.05648253242970.321722851782-0.3271001849170.09589102690170.0794885525642-0.1612411280120.216354866214-0.15196196257-0.1223633801170.239819236440.03996003595880.0421164154060.304246586055-0.03552473254780.226953331348-14.45485595983.9343764585845.7661336859
22.432547977250.2840242613860.5020161807792.778178877580.8641427620353.097764426670.0714537219560.0520102510944-0.331479717368-0.1241931675430.0829863829407-0.02828998908290.7836779082750.0136773284977-0.1493167759350.4318053137010.01065508399410.009936701420570.2263755522460.07311650342340.250589922024-2.63745561542-37.068225095726.5517293792
30.874438632602-0.0153374822298-0.9015236936690.8724588439420.4697332622424.018969930740.154175489606-0.04399414698640.09996567855750.08177348375130.2085922880790.007698858593150.172811620208-0.374672667732-0.2925453269170.3376216843020.0160838551828-0.01231804664380.2472189968750.03501391389950.239992154416-6.4417657223-24.084899795529.3245011121
40.9536880028430.12155254199-1.911061883970.9783194101951.490521855642.090857747070.0821456839756-0.0718756625450.0799215068573-0.09887478709940.142484574914-0.08875731229960.1515504334290.486132049921-0.2878766296420.3729527354310.00510558842311-0.0207027010980.364653979933-0.01213844618270.275475715148-3.32468591019-24.115933705825.8537684228
54.11829594490.1194993631720.01362255120510.768168529179-0.02703634470550.673072032560.06731176705640.2232378053160.185470169327-0.0362718046836-0.08804073457240.0254890687015-0.0460492486530.08476664083810.02608309282950.2512157652110.06824943641850.01578783642320.2754853026830.01948388780970.17272330242539.6988489689-13.55314170144.3402780998
61.15719914084-0.5847200007150.1541240359783.13564562733-2.255396263691.56629640521-0.2598247771350.379601811878-0.0346675333667-0.2490580344850.4261433284490.380877764401-0.262106270922-0.46496275916-0.1627253374460.783344358907-0.0496705760092-0.163091015780.688134932089-0.02768980.54817541016845.362523063330.033914684530.0039096041
73.18421600523-0.0875764250052-0.2807051299351.26251916989-0.1657546652692.248253036760.02267458299290.05866995647720.0630227580722-0.08354900884380.002767253780430.232494016360.10178822127-0.82918551077-0.01910729003780.238926584966-0.0730997074251-0.01466470333990.5286543596760.004526019762130.20506977316352.3323646371-14.096926523411.3732346927
80.9052570184320.794685624202-0.5236794921082.627629716021.043517826641.59502250774-0.1180437113560.01674326580130.1224747725630.3696952607530.310326561939-0.146626985059-0.2061690060250.223559868307-0.1791320662420.894759203121-0.0570737278014-0.1494152559720.8291984030180.0828634222710.61603689441847.629627712236.738356545829.767173267
90.0277532358526-0.0650530153488-0.01239815797290.6616330524421.731332966724.063099965350.3414211980480.305200461494-0.08865544761510.09644504174150.0003759995962660.02772511764491.49489775425-0.179887184913-0.2963918203440.973634813924-0.011187192007-0.06535892477790.964168653160.007067134346690.44317172703246.609683935424.193423492429.808885571
100.1039442922710.167870515668-0.6994820306990.188853614989-1.258420204096.158490930820.30736906196-0.038379412246-0.144310055946-0.111701049154-0.06571330793470.06910864819541.184863199060.212553102163-0.1960371887490.8133335364130.0399463465004-0.06988433666020.898301248365-0.008880062548190.4062222526445.023454501424.135302898425.8536889574
119.61296412276-0.6193738318030.7879270688954.746580696490.4405453020684.513480900510.156666769662-0.8502839709960.1069431263250.3075660305040.05663010039070.649976209371-0.262553369563-0.667108668564-0.1913094029460.309597110620.05464676443230.08770749121480.3716457219180.04343834467240.233532005232-21.006916003618.682671492218.7826120028
124.562536334990.873176709527-0.1494699364923.08505777813-0.1942182331622.73178561630.05312354181480.112660250751-0.243001967041-0.2677769197750.04706306465570.3179809912880.0806440522294-0.257812061471-0.08083381651760.2340998136510.0367410081610.000246451212960.1732168447660.0007480661621570.204524231815-12.894588039711.21928437686.55681694806
132.53670360256-0.266547785758-0.3018800890312.737145653720.8749898210952.591107608110.0474575347857-0.2824952975050.136371408176-0.07417015967510.0654040219256-0.485033475266-0.2471134162280.571221354119-0.1074590635750.258676060253-0.07991746433740.05783533075640.3567050843340.04286256173230.26883762845611.179228839616.010720930714.0329432181
144.25572594923-0.213124536794-0.7278513995342.06805369967-0.2770230310922.08098567230.2091298109960.1288936373730.358763663324-0.236142382378-0.04271953777850.194713476367-0.455685088829-0.127445881524-0.1651886698540.3728733254450.01804877317190.01425385192740.2147805702340.03924316741990.194493553091-10.282200484621.19664361466.54924541321
152.73392135956-0.2769387531010.1898803582232.098876861061.240174893722.396275641640.0638818754066-0.310308231927-0.412433982112-0.133333851872-0.111422563913-0.1632302371160.3262841919270.2777881956740.02873137521250.237440287766-0.003409739226450.07480686130420.2696391687660.08049856199440.2693336484193.920739139834.15542931859.9544677186
162.97850456149-1.375121538550.7666056329772.24754102118-6.786541876859.44273638260.0783106903018-0.108302022339-0.0482460977043-0.1254958047750.1064073411060.2975427834440.547240470896-0.164122261246-0.2581312054090.297970266778-0.0204909485643-0.01144712005150.161397311238-0.01320031178730.17965322025-13.0258750506-29.300425672922.2682753753
175.46081945259-0.542920902025-0.6792200750535.016273785341.847453301842.89619930445-0.223798218144-0.593061524506-0.9894489448540.472556123620.0972033041534-0.09690448249051.165782596790.3078882382240.1293990781540.7911865245010.115757906964-0.008269026333350.330885813590.09751492263390.410732421681-1.30810426766-44.249209781634.7382787945
182.077191193970.0761901521730.3290697764344.5819310364-0.5437387975735.469587810460.09113195565370.6820657652960.0881233390053-0.201024757565-0.0411995169338-0.64613023647-0.2777933593320.541639317867-0.02658958816420.319823939123-0.02524300344190.04313413859510.369745939731-0.005242358076180.3369793344429.9462529286919.254860798636.8604872733
194.58499105940.279833149491-0.06663391375943.793060833860.6136430957433.590287976980.05441187631670.0365300705063-0.4555823454170.3114967778150.0430365706854-0.2604923787030.4976285986790.367583708482-0.1425027801490.2600606897550.0316502942789-0.05856126734190.2521788578980.002747709282490.2484290066734.836712183119.5940624736749.60429569
202.8565229570.32562388922-0.02478340417891.34260031852-0.1346971821752.11944838082-0.02696876072790.1520886103720.1902684192380.1016058694050.1336473760750.247821418774-0.224854861311-0.521953917345-0.1121385014920.303593690980.07735612702540.04890336276570.3540872305390.01868862053050.218318742916-17.067701797315.836761670643.5333179818
217.32019004366-0.2259850551180.1431190570622.69479034431-0.5524730132753.745310930120.0652677659809-0.04568528912181.064736704470.1417516387030.0835069936327-0.167851650363-1.087736374640.139463038663-0.1398794321330.508536653187-0.01964076356520.01463040245360.21023210158-0.0166352925650.3505143905190.15526366425228.739961506749.111020118
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid -33 through 26 )DC-33 - 26316 - 375
22chain 'D' and (resid 27 through 88 )DC27 - 88376 - 437
33chain 'G' and (resid -3 through 11 )GE-3 - 11
44chain 'H' and (resid -3 through 11 )HF-3 - 11
55chain 'A' and (resid -347 through 4 )AG-347 - 41 - 352
66chain 'A' and (resid 5 through 88 )AG5 - 88353 - 436
77chain 'B' and (resid -347 through 26 )BI-347 - 261 - 374
88chain 'B' and (resid 27 through 88 )BI27 - 88375 - 436
99chain 'E' and (resid -3 through 11 )EK-3 - 11
1010chain 'F' and (resid -3 through 11 )FL-3 - 11
1111chain 'C' and (resid -348 through -306 )CA-348 - -3061 - 43
1212chain 'C' and (resid -305 through -230 )CA-305 - -23044 - 119
1313chain 'C' and (resid -229 through -103 )CA-229 - -103120 - 246
1414chain 'C' and (resid -102 through -34 )CA-102 - -34247 - 315
1515chain 'C' and (resid -33 through 26 )CA-33 - 26316 - 375
1616chain 'C' and (resid 27 through 54 )CA27 - 54376 - 403
1717chain 'C' and (resid 55 through 88 )CA55 - 88404 - 437
1818chain 'D' and (resid -348 through -306 )DC-348 - -3061 - 43
1919chain 'D' and (resid -305 through -243 )DC-305 - -24344 - 106
2020chain 'D' and (resid -242 through -66 )DC-242 - -66107 - 283
2121chain 'D' and (resid -65 through -34 )DC-65 - -34284 - 315

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