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- PDB-7erb: Crystal structure of human Biliverdin IX-beta reductase B with At... -

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Basic information

Entry
Database: PDB / ID: 7erb
TitleCrystal structure of human Biliverdin IX-beta reductase B with Ataluren (PTC)
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / platelets / Biliverdin reductase B / BLVRB / inhibitors / NADP / Ataluren
Function / homology
Function and homology information


biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process ...biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-JBF / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGriesinger, C. / Lee, D. / Ryu, K.S. / Kim, M. / Ha, J.H.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IX beta Reductase B as a Novel Thrombocytopenia Therapeutic Target.
Authors: Kim, M. / Ha, J.H. / Choi, J. / Kim, B.R. / Gapsys, V. / Lee, K.O. / Jee, J.G. / Chakrabarti, K.S. / de Groot, B.L. / Griesinger, C. / Ryu, K.S. / Lee, D.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
C: Flavin reductase (NADPH)
D: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,28018
Polymers88,5934
Non-polymers4,68714
Water17,907994
1
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6409
Polymers44,2972
Non-polymers2,3437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-39 kcal/mol
Surface area17120 Å2
MethodPISA
2
C: Flavin reductase (NADPH)
D: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6409
Polymers44,2972
Non-polymers2,3437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-47 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.423, 117.338, 82.045
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
Flavin reductase (NADPH) / FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / ...FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / GHBP / NADPH-dependent diaphorase / NADPH-flavin reductase / FLR


Mass: 22148.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-JBF / 3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid


Mass: 284.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H9FN2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 994 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.9-2.0M Ammonium sulfate, 0.1M Bis-tris(pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.5→41.71 Å / Num. obs: 128178 / % possible obs: 99.36 % / Redundancy: 9.4 % / Biso Wilson estimate: 10.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.77
Reflection shellResolution: 1.5→1.555 Å / Rmerge(I) obs: 0.4377 / Num. unique obs: 12462 / CC1/2: 0.818

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Processing

Software
NameVersionClassification
HKL-20001.16_3549data collection
HKL-20001.16_3549data scaling
PHENIXmodel building
PHENIX1.19.2refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HE5
Resolution: 1.5→41.71 Å / SU ML: 0.1517 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.4956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 2004 1.56 %
Rwork0.1708 126060 -
obs0.1712 128064 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 306 994 7512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01446733
X-RAY DIFFRACTIONf_angle_d1.48099236
X-RAY DIFFRACTIONf_chiral_restr0.08891071
X-RAY DIFFRACTIONf_plane_restr0.00971165
X-RAY DIFFRACTIONf_dihedral_angle_d12.53445319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.30251410.27338672X-RAY DIFFRACTION96.68
1.54-1.580.28951360.25818885X-RAY DIFFRACTION99
1.58-1.630.2851470.23298926X-RAY DIFFRACTION99.4
1.63-1.680.23061380.21678935X-RAY DIFFRACTION99.46
1.68-1.740.23621390.20178962X-RAY DIFFRACTION99.56
1.74-1.810.23081400.18848953X-RAY DIFFRACTION99.69
1.81-1.890.20391490.17478954X-RAY DIFFRACTION99.37
1.89-1.990.17841420.16299012X-RAY DIFFRACTION99.77
1.99-2.120.17811410.15549018X-RAY DIFFRACTION99.73
2.12-2.280.19791440.14789034X-RAY DIFFRACTION99.76
2.28-2.510.15881420.14889059X-RAY DIFFRACTION99.61
2.51-2.870.17231450.15359114X-RAY DIFFRACTION99.82
2.87-3.620.1751500.14879160X-RAY DIFFRACTION99.65
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)
12.714439977451.603507519790.8671665721696.06120578416-0.821757185572.16182115507-0.2368053781480.182207340348-0.0140569151717-0.1481297385830.0874046620891-0.3106529826520.155440197890.350758458990.1300700985310.06855454084490.00575723988218-0.01777033464410.119896494412-0.0104204866290.045783474952915.0384484928-35.723133828821.3408814434
23.122497738340.449909452630.04790714986371.03233871522-0.2368020164172.45149778058-0.04594731615490.162810686562-0.128271748846-0.002599618251180.0380445052375-0.08378618341710.2854935514730.2262705634740.006145135529890.1106476427130.04117472147610.001047157815140.0637890034843-0.003736983113970.08542614931711.9568025195-40.66388641819.5938969484
32.468973960691.217637613260.3234042820521.31776913051-0.3985590477950.482901599824-0.356170822114-0.00620914327072-0.80874646543-0.1372725534930.132224065624-0.07080308350250.8527845368210.05925165199940.1445068346430.3453610161570.05197322446970.04833566733420.1472825270890.02707787238790.2565528381299.42278594649-46.938906666128.3141320473
41.43129283676-0.124740877696-0.2510304143290.974973670260.2690863079621.74758139923-0.0786331835384-0.14113307368-0.08169168404810.1596737125780.03259788143160.01824773582720.1914627673110.03961483114110.0207613816980.07460962236255.52433546583E-50.004587430982150.06926922269650.001892380622860.06853387761677.27456724143-33.383795054830.1902951673
54.055202539040.4071510397870.4361054436250.9116406415490.4440794262512.01120504346-0.0528927795390.06042438021320.1664490294050.0247036727457-0.002034955810590.012249823393-0.05793071277330.02886407565570.06196372712960.0491744755282-0.0007398139141290.005412201674960.02867413525340.006310138365790.06631293585172.73267734501-24.435467753323.5082949434
66.966959709691.84715334280.3789358368791.750206309720.6502889239081.235445459860.00224242043277-0.1798534575290.130969506906-0.0107985629193-0.07852974169630.0481677187774-0.01331040543-0.1764062703960.05566228250250.0415166325410.008819303982890.006554832340320.0930401351079-0.01614818151950.0812751089966-3.75752748774-23.170826554824.5319200714
70.629530621680.102046664467-0.0360792747761.503610009440.9963743829251.995366535020.02129297864020.0614806307992-0.0173859997369-0.105907589925-0.03376014581970.02822500523370.0873780552567-0.1731155569620.01385196570090.0706325235065-0.0149278488858-0.003801684266080.06930250240990.003185171707020.062798752290.613943895204-30.228349038410.4175452664
84.248066585531.548709755261.04318271913.677806564360.6302896792522.20492052356-0.1298184872170.0424796937840.0704468839295-0.1915228091080.0334582780665-0.1120123498910.01848980360740.09360709928610.09994961467890.07035470705470.006288358396320.01024336851960.06789596064150.001085828795780.04977751491416.41872716108-34.820610159111.2943613331
92.15045351633-0.03765761263-0.06512670280582.48647784539-0.03226935911711.37603373598-0.0397238418140.1654838936410.143891611583-0.287009646761-0.03304660104930.086009147939-0.01937275386380.05790806724250.03114231448470.0992063786918-0.01665193613050.0167086987410.1210062160070.02625173710010.05036491396214.18826253377-27.9658718047.64357066363
101.657212917340.3416950072960.6365081310065.65437520711-0.1736744901823.79082601850.04267999522310.0772216417194-0.004658235020230.133844722242-0.04804982274290.0890492940635-0.243786343101-0.1763522144010.03018081048110.1757996597940.0279669214926-0.003726495793110.07059499469040.01152477846360.0953632947888-3.850754626742.9897298457635.2093628042
111.98827910651-0.2583163644010.7934161641214.78473035566-2.702513575793.840738463670.06142529615780.0199818127921-0.06763495171190.148910508025-0.301991641416-0.868561086843-0.1485703496730.3687158533240.2925997633470.25287147303-0.00275999290792-0.03971732482150.1196364787160.03212425346950.2305366898644.013023109311.9800352063941.0299027515
120.6173007982020.297373826964-0.2860234976974.17208297943-0.1837049349381.456898156010.0343021804266-0.0107655160090.05540105799660.306404553726-0.0476738586750.0623763615012-0.310312131961-0.2051903673150.02367900838190.1589279206510.04268314617450.01873252072150.136357328769-0.006910615004790.086299956777-8.8065005343-7.640136280744.3580319075
130.352623080040.509263013846-0.4278683338723.71020211601-0.2607560061472.53010357648-0.03563440061030.03962834244510.06989877793810.1849928078110.1243911955320.119263407129-0.0901854401897-0.291302449551-0.05838178214760.06426956752840.001200711517490.0009239509165980.170226747407-0.01010742233850.112884794578-13.1343019903-12.572703236841.4585639685
141.095971533870.315030908585-0.7500197023761.62496834523-0.2031927176410.865753426026-0.2488147173680.39289299628-0.328246617086-0.6872424723390.3557199646720.1756431895990.167647732609-0.80614640325-0.1619721513650.319561861224-0.0515891720431-0.09480118872550.5343537061630.05812520769860.184809440271-14.1404777649-9.4181862563824.113119865
153.091129702351.35588264222-0.163815813622.68121180698-0.4221660782890.63180072241-0.1315307838680.6519201906410.271820100699-0.5706727148290.4326925289960.273639528146-0.351605218787-0.830388912028-0.007208889199660.229641574380.0583515321563-0.04668212085140.4168059796170.03652018579670.128693367104-13.5422009515-4.2196614928328.5030589427
163.4520204038-0.8392504528210.1316088998764.2304849387-0.7362534142722.07650924236-0.261617375607-0.1746577574330.06164778718250.08536208142020.17883522505-0.353089228759-0.1068459343630.3480229029030.1389674525870.03540313345580.007248922585680.004223976731280.131839624715-0.02520111616480.081297753157414.7094300957-22.57706114460.8289736663
171.65208741547-0.395006128658-0.5126957793671.266356483970.3184037013952.71553857732-0.0573209521005-0.006650642474730.09352391234360.0001348223492020.0969210813242-0.126909630868-0.1897637387370.197619603565-0.02977672086890.0649284880945-0.02175678398060.0001846193223790.0506672315270.002448489033310.084180747906811.3332931905-17.796788565562.7321363304
184.297122952690.540415615521.621763676611.04116272439-0.4170347981561.80795993186-0.6489209505920.1220938290121.00548371182-0.07188056142530.2415064087970.240429578562-1.176151021820.07122298269720.2087994171050.354738930919-0.0532247660515-0.06764550436750.1739683899920.05204907718410.3076995201228.17488003418-11.574783065154.2969773105
192.11117454890.311103267650.5370259819010.7404106709650.2991123469011.59543716356-0.04115245263110.1355254216380.0687750003434-0.1408584198540.0391751814951-0.0104271657068-0.09101454093080.1166104342560.0001390568747990.0674771651837-0.004592298469320.002667308673270.06205859079190.001399168071440.06778680407336.941919811-25.174496542852.0306382719
204.39872269792-2.73425022815-0.3681229384913.621083365960.3505244686333.02950123283-0.02598645017590.212848358065-0.0314171229594-0.0601304340445-0.0107973346004-0.01496599742170.08972557383110.181956686268-0.00490678927920.0650663124217-0.01238803008270.01738365103220.0729457444621-0.005904003223410.06423839848789.07778348309-33.705510473551.5131854244
213.81415102364-0.166325433051-0.7997131558081.555644404130.1518654764521.94027357101-0.0494591784605-0.165682666942-0.112611828710.0802001266280.03222034755240.1264569032620.206871080852-0.1463557629890.05692767456310.0728866816783-0.005484430328890.003215968041130.07078326480390.009528715477270.0608730010144-1.73474360077-34.780059954264.2801970343
227.30809391835-2.3531087105-0.3530356212052.238353269980.6822732053521.444889538830.01845728663820.0720251515777-0.03227249793080.0364421103153-0.05675099199950.03915360486110.14198375602-0.1374874928580.03855943671770.0529022246683-0.0167625398757-0.002130903136370.0669427063337-0.0098803904910.0681412192278-3.54304890184-35.986723988257.6208576347
230.628352007374-0.1530629170250.04505329099611.49498681920.8991883633681.967453815180.0254876312953-0.0671017961463-0.03301947290680.162558185366-0.05788408684470.06683187347430.124143687285-0.1483545482770.03162983974310.05977538722320.005554429880350.00737428559750.0618975807451-0.002151347065560.07419109021770.534403526802-28.917247768171.7687782132
246.96945535005-2.4721455235-1.666175213182.872520272111.132416107582.14615552258-0.117224979817-0.0538811913937-0.08830192066710.1218861582370.0289161963756-0.1679183344350.03551209448720.107410245770.08388884633420.04637519507230.00809010361622-0.006350336440170.0522724746398-0.003640193542630.0600567852236.11973668008-24.035647560670.9286453461
252.61216592229-0.1237258919480.1081558260343.78011375686-0.1990921122391.68936453749-0.00265391324682-0.0976289723065-0.1187171678880.277842227552-0.0437083200442-0.01095008477560.1510272368590.06992278827680.02616735517390.1063595953040.0116669664948-0.02840019012630.1009940170880.01619416649430.03639915896693.80086875713-30.61211285674.691235343
261.83505055605-0.424083623229-0.9649239607053.7533144687-1.148193501063.235085737720.0229146155217-0.008772506446530.0680490323582-0.185095603526-0.0584164419831-0.2571042848970.00484414697320.1744040872840.05934492832570.127412205701-0.02139809577910.00171128141430.06302214723260.009453239198980.1115345338661.55771955035-61.327895649443.6104242728
270.609227919686-0.4803626271990.2209635702144.18948354714-0.07877912002930.9301052263520.03279009924730.0192906929258-0.0541341164706-0.3479691165380.008335459138930.1549159809190.198151443979-0.142356176683-0.02131854661150.149644354964-0.0438260601889-0.03596029183060.1036542765590.007715507896790.0891687031807-7.95195521748-51.41210068337.733338434
280.966881027189-0.529826421810.1865212122122.97930557064-0.6350341496111.45799926755-0.0569515343302-0.210630614766-0.0380336156940.2657511903030.2498874959070.3655595518440.0212529704356-0.264555927952-0.1071108795780.117159138002-0.006390601929380.02260441068950.1741281684540.028790055060.157131475991-12.8942185108-47.879608798946.586816697
293.43828635589-0.734645202381-0.6000597791853.17449994501-0.4220973087810.732192642805-0.135077419444-0.461344405184-0.2728721296650.6773909697280.4206376002760.4883118897630.176434822239-0.353035476555-0.06664303417180.2124856274230.01397141271930.05874423239230.2153373421150.06912072274890.170855535082-12.96593192-55.496993820953.3409407141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 48 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 142 )
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 190 )
9X-RAY DIFFRACTION9chain 'A' and (resid 191 through 206 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 122 )
13X-RAY DIFFRACTION13chain 'B' and (resid 123 through 155 )
14X-RAY DIFFRACTION14chain 'B' and (resid 156 through 174 )
15X-RAY DIFFRACTION15chain 'B' and (resid 175 through 206 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 13 )
17X-RAY DIFFRACTION17chain 'C' and (resid 14 through 34 )
18X-RAY DIFFRACTION18chain 'C' and (resid 35 through 48 )
19X-RAY DIFFRACTION19chain 'C' and (resid 49 through 85 )
20X-RAY DIFFRACTION20chain 'C' and (resid 86 through 101 )
21X-RAY DIFFRACTION21chain 'C' and (resid 102 through 122 )
22X-RAY DIFFRACTION22chain 'C' and (resid 123 through 142 )
23X-RAY DIFFRACTION23chain 'C' and (resid 143 through 174 )
24X-RAY DIFFRACTION24chain 'C' and (resid 175 through 190 )
25X-RAY DIFFRACTION25chain 'C' and (resid 191 through 206 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1 through 57 )
27X-RAY DIFFRACTION27chain 'D' and (resid 58 through 122 )
28X-RAY DIFFRACTION28chain 'D' and (resid 123 through 174 )
29X-RAY DIFFRACTION29chain 'D' and (resid 175 through 206 )

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