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- PDB-6r2o: Hemoglobin structure from serial crystallography with a 3D-printe... -

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Basic information

Entry
Database: PDB / ID: 6r2o
TitleHemoglobin structure from serial crystallography with a 3D-printed nozzle.
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / Serial Crystallography / LCLS
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsOberthuer, D. / Yefanov, O. / Sarrou, I.
CitationJournal: Nat Commun / Year: 2020
Title: Ultracompact 3D microfluidics for time-resolved structural biology.
Authors: Knoska, J. / Adriano, L. / Awel, S. / Beyerlein, K.R. / Yefanov, O. / Oberthuer, D. / Pena Murillo, G.E. / Roth, N. / Sarrou, I. / Villanueva-Perez, P. / Wiedorn, M.O. / Wilde, F. / Bajt, S. ...Authors: Knoska, J. / Adriano, L. / Awel, S. / Beyerlein, K.R. / Yefanov, O. / Oberthuer, D. / Pena Murillo, G.E. / Roth, N. / Sarrou, I. / Villanueva-Perez, P. / Wiedorn, M.O. / Wilde, F. / Bajt, S. / Chapman, H.N. / Heymann, M.
History
DepositionMar 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,71812
Polymers62,0654
Non-polymers2,6548
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-136 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 80.800, 110.800
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 7 or resid 9...A1 - 7
121(chain 'A' and (resid 1 through 7 or resid 9...A9 - 81
131(chain 'A' and (resid 1 through 7 or resid 9...A83 - 87
141(chain 'A' and (resid 1 through 7 or resid 9...A90 - 91
151(chain 'A' and (resid 1 through 7 or resid 9...A93 - 104
161(chain 'A' and (resid 1 through 7 or resid 9...A106
171(chain 'A' and (resid 1 through 7 or resid 9...A108 - 115
181(chain 'A' and (resid 1 through 7 or resid 9...A117 - 140
191(chain 'A' and (resid 1 through 7 or resid 9...A142
2101(chain 'C' and (resid 1 through 7 or resid 9...C1 - 7
2111(chain 'C' and (resid 1 through 7 or resid 9...C9 - 81
2121(chain 'C' and (resid 1 through 7 or resid 9...C83 - 87
2131(chain 'C' and (resid 1 through 7 or resid 9...C90 - 91
2141(chain 'C' and (resid 1 through 7 or resid 9...C93 - 104
2151(chain 'C' and (resid 1 through 7 or resid 9...C106
2161(chain 'C' and (resid 1 through 7 or resid 9...C108 - 115
2171(chain 'C' and (resid 1 through 7 or resid 9...C117 - 140
2181(chain 'C' and (resid 1 through 7 or resid 9...C142
1192(chain 'B' and (resid 1 through 7 or resid 9...B1 - 7
1202(chain 'B' and (resid 1 through 7 or resid 9...B9 - 15
1212(chain 'B' and (resid 1 through 7 or resid 9...B17 - 19
1222(chain 'B' and (resid 1 through 7 or resid 9...B21 - 71
1232(chain 'B' and (resid 1 through 7 or resid 9...B74 - 78
1242(chain 'B' and (resid 1 through 7 or resid 9...B80 - 81
1252(chain 'B' and (resid 1 through 7 or resid 9...B83 - 88
1262(chain 'B' and (resid 1 through 7 or resid 9...B90 - 91
1272(chain 'B' and (resid 1 through 7 or resid 9...B94
1282(chain 'B' and (resid 1 through 7 or resid 9...B96 - 103
1292(chain 'B' and (resid 1 through 7 or resid 9...B106
1302(chain 'B' and (resid 1 through 7 or resid 9...B108 - 137
1312(chain 'B' and (resid 1 through 7 or resid 9...B140 - 141
1322(chain 'B' and (resid 1 through 7 or resid 9...B144 - 145
1332(chain 'B' and (resid 1 through 7 or resid 9...B147
2342(chain 'D' and (resid 1 through 7 or resid 9...D1 - 7
2352(chain 'D' and (resid 1 through 7 or resid 9...D9 - 15
2362(chain 'D' and (resid 1 through 7 or resid 9...D17 - 19
2372(chain 'D' and (resid 1 through 7 or resid 9...D21 - 71
2382(chain 'D' and (resid 1 through 7 or resid 9...D74 - 78
2392(chain 'D' and (resid 1 through 7 or resid 9...D80 - 81
2402(chain 'D' and (resid 1 through 7 or resid 9...D83 - 88
2412(chain 'D' and (resid 1 through 7 or resid 9...D90 - 91
2422(chain 'D' and (resid 1 through 7 or resid 9...D94
2432(chain 'D' and (resid 1 through 7 or resid 9...D96 - 103
2442(chain 'D' and (resid 1 through 7 or resid 9...D106
2452(chain 'D' and (resid 1 through 7 or resid 9...D108 - 137
2462(chain 'D' and (resid 1 through 7 or resid 9...D140 - 141
2472(chain 'D' and (resid 1 through 7 or resid 9...D144 - 145
2482(chain 'D' and (resid 1 through 7 or resid 9...D147

NCS ensembles :
ID
1
2

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15138.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P01958
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15894.128 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02062

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Non-polymers , 5 types, 66 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Source: (natural) Equus caballus (horse)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: batch mode
Details: in 26% PEG3350,10mM Hepes pH7.5, ratio 1:2, Stirring, O.D 10

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.734 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.734 Å / Relative weight: 1
ReflectionResolution: 2.46→20 Å / Num. obs: 21072 / % possible obs: 100 % / Redundancy: 1059 % / Biso Wilson estimate: 40.7 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.11
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 99.5 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2074 / CC1/2: 0.7 / R split: 0.538 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec. / Pulse photon energy: 7150 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: 3DP-DFFN in air / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: Proteinbuffer / Description: 3DP-DFFN / Filter size: 20 µm / Flow rate: 7 µL/min / Injector nozzle: 3DP-DFFN / Injector temperature: 293 K / Power by: Elveflow
Serial crystallography data reductionCrystal hits: 140443 / Frames indexed: 114958

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CrystFEL0.6.3+39640b93cddf9ab9272351cc7917fc158cd4d010data reduction
CrystFEL0.7.0+7754d197data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8K

1y8k


Resolution: 2.46→19.87 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.2563 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.212 1868 8.91 %
Rwork0.1657 19099 -
obs0.1698 20967 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.46 Å2
Refinement stepCycle: LAST / Resolution: 2.46→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 182 58 4626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334894
X-RAY DIFFRACTIONf_angle_d0.61996722
X-RAY DIFFRACTIONf_chiral_restr0.036710
X-RAY DIFFRACTIONf_plane_restr0.0032860
X-RAY DIFFRACTIONf_dihedral_angle_d14.99382790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.530.29351420.25131449X-RAY DIFFRACTION100
2.53-2.60.26321420.23221445X-RAY DIFFRACTION100
2.6-2.680.26171420.20661447X-RAY DIFFRACTION100
2.68-2.780.27171390.19891435X-RAY DIFFRACTION100
2.78-2.890.22891420.19461449X-RAY DIFFRACTION100
2.89-3.020.25321440.1971461X-RAY DIFFRACTION100
3.02-3.180.23961400.19111442X-RAY DIFFRACTION100
3.18-3.380.22351440.18161474X-RAY DIFFRACTION100
3.38-3.640.22991430.15891460X-RAY DIFFRACTION100
3.64-40.18561440.13571468X-RAY DIFFRACTION100
4-4.580.1741450.12391485X-RAY DIFFRACTION100
4.58-5.740.17071470.14231507X-RAY DIFFRACTION100
5.74-19.870.20161540.16421577X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.944630293373.26770777645-3.144704895964.53218669253-1.629784476154.498395091440.1667297341590.3504439411050.50817811847-0.102690548540.3466539846360.355261687372-0.146922460576-0.334977867302-0.484241862330.2874762949610.02179497072010.01571068918110.3541576786560.05316787341320.4432457675553.8674003563587.11160215233.4726199042
26.759283370260.0829776402182-1.711739881532.2522649128-0.7458937726166.561577820440.04506887592150.882690202220.402299669531-0.240686935990.4542359368750.135167098708-0.0254052041911-0.555318893577-0.5049098171370.326463892524-0.0101385982945-0.05689325969560.5628180230420.02509496634690.3870322154327.548375288585.727850108123.7711204007
36.392236906110.386086432785-3.223756152922.33970397563-0.4543434710617.07755084830.1119734653640.3326371474970.233424563961-0.1814539218370.002868272511260.2200044752150.3028358098470.0529818088264-0.07131008582410.2068274773850.0175790673859-0.06909332215770.275090006641-0.02180710499130.2787873809568.6510206526882.94696678134.1102051671
47.286051667334.73363507153-1.510235730836.53372120938-2.135204072033.12326094832-0.2372760066680.0817833643752-0.003204437189630.04099022009070.170845783578-0.471498813073-0.4683392733090.3278939913770.01892940286180.898386562054-0.2214128025390.3638119058960.523086789031-0.2461350689830.91469424884111.0693103171106.08572031949.6989956266
52.644376968120.2327697257631.319138812594.31384002836-1.806687630915.050705384080.285775707421-0.4033393292050.4075419532350.8488517356260.0666640126880.495299200871-0.0921299335651-0.0425224408037-0.3904888409430.407132741197-0.0221352751990.1468521262530.403494911792-0.050307533460.4302268312834.3323702571781.667760662555.9612582821
63.289272297951.70017089408-1.898851001916.82320405213-3.074804241294.720305135080.302258050655-0.7910338617730.5136684347380.641752975262-0.284734205147-0.181322773032-1.012134283350.163435855922-0.2759311514370.683345234242-0.06601813553170.2168074909370.657870185984-0.2342556361240.5970087880788.4237987355992.21935402460.6679387677
72.73094658572-0.612840669035-0.3082228956862.674998319932.821012125444.945094382850.147409128023-0.4884877575170.6653827076071.357356677680.399854821228-1.05340349427-0.3722799133161.61129600849-0.4521616190640.701444820181-0.126113145888-0.003182188631420.892955083205-0.2519845552190.6510228951422.328357890189.531294939459.135395608
83.76817776383-1.36314765720.9217929954933.665678985540.1430674851514.610943726130.4598588806710.1580946729520.9803061319950.550722554948-0.3076385876590.150381989002-0.380829536952-0.0544140590988-0.2070845014840.364168503512-0.02103453992040.1930640293670.358075641803-0.07488357156490.5445715855297.5033272894190.974852537147.4425587441
92.76433266502-0.6827664955323.966084146384.98252758825-2.625189495547.391030213630.451899510349-0.3530688657490.2149756683440.3798571502440.0519914259075-0.302385226152-0.4016678275020.53046184342-0.509604241470.559897830337-0.1858832562170.1865023141520.582253480374-0.2243339272390.55795351606416.84250758395.039803737648.4385103664
102.163864980230.0284341792434-0.2583145236882.340027031630.7909610882266.0711175814-0.0659152873209-0.0388427659202-0.187248166532-0.123330520379-0.01958837443240.06117122378680.03432408280610.08835846798620.07924368026710.352327950498-0.0627959617494-1.12450809078E-50.2068468580040.01557220826160.31266791621928.59227947963.139736862441.6044457765
113.07398113557-1.218209595850.1273711603934.80885245173-0.5008883114014.21576197887-0.0670048027579-0.127321224343-0.3840493682950.2657861522190.01172575010840.1603426288570.386190839172-0.246280782380.07691498434740.423832751654-0.09728511563940.06982275126410.2960813546690.01937157407160.43203508534821.526515026158.752364915346.9850897159
123.8444229307-0.438906076992-1.472791306974.1731036123-0.2448078714474.78609231665-0.03111316385140.18376719186-0.297025850516-0.04041830378970.08263924713180.1617776831250.139877195481-0.456093205875-0.05650628370270.2811002555-0.0378762068408-0.01290604828030.192995875126-0.008424005519390.25710494028124.363742801867.288864079240.3507288383
135.06535909097-0.3973849312383.227444388253.62438633234-1.321626969254.180672930720.0382590430035-0.2269895810090.2051347322620.394163281102-0.222723907674-0.453791440508-0.1542713807040.09716326309190.2161509663280.210638841509-0.03868826202270.003137914026730.2772649623090.009247943075640.27131171469539.910303890780.320642112136.4756109358
144.136336974380.8413669517451.643096858244.46323610162.277983738.80296374588-0.02630650479370.2856495896630.203376751258-0.693712217368-0.0756079084115-0.284837096816-0.2173218570210.1425675297040.12562408490.2856856860310.03737201558890.06571226078470.3150226855010.07456489142790.30246789444540.805066227582.890926732528.6067757448
152.3232703143-0.03843827636240.2530397998132.95041093636-0.9336967585582.920088046920.0191482503719-0.2635354506610.3092971419450.485879589513-0.0598470602446-0.0331914545897-0.4093762576930.128396632270.0329712064790.27321562858-0.06632226351150.02221369489010.2566930628-0.0143321881380.23592799447636.213697409784.578773072642.1391998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 141 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 16 )
5X-RAY DIFFRACTION5chain 'B' and (resid 17 through 57 )
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 76 )
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 121 )
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 145 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 43 )
11X-RAY DIFFRACTION11chain 'C' and (resid 44 through 88 )
12X-RAY DIFFRACTION12chain 'C' and (resid 89 through 141 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 45 )
14X-RAY DIFFRACTION14chain 'D' and (resid 46 through 75 )
15X-RAY DIFFRACTION15chain 'D' and (resid 76 through 146 )

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