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- PDB-12rh: Structure of turkey hemoglobin A covalently bound with epigalloca... -

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Basic information

Entry
Database: PDB / ID: 12rh
TitleStructure of turkey hemoglobin A covalently bound with epigallocatechin gallate
Components
  • Hemoglobin beta chain
  • Hemoglobin subunit alpha-A
KeywordsOXYGEN TRANSPORT / caffeic acid / antioxidant
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-KDH / Hemoglobin subunit alpha-A / Hemoglobin beta chain
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsBingman, C.A. / Yin, J. / Smith, R.W. / Richards, M.P.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2014-67017-21648 United States
CitationJournal: J.Agric.Food Chem. / Year: 2026
Title: Oxidative Characteristics of Turkey Hemoglobin A Containing Covalently Bound Epigallocatechin Gallate.
Authors: Yin, J. / Zhang, W. / Tatiyaborworntham, N. / Bingman, C.A. / Richards, M.P.
History
DepositionApr 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,96511
Polymers62,4864
Non-polymers3,4797
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-114 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.000, 81.600, 90.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 14913.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: G1N9H8
#2: Protein Hemoglobin beta chain


Mass: 16329.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P84479

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Non-polymers , 4 types, 375 molecules

#3: Chemical ChemComp-KDH / (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate / (-)-Epigallocatechin-3-gallate / EGCG


Mass: 458.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: THE CONCENTRATION OF HB-EGCG ADDUCT WAS 16 MG/ML IN 10 MM TRIS PH 8.0. THE CRYSTALLIZATION RESERVOIR WAS 20% PEG3350, 0.1 M RACEMIC MALIC ACID, 0.05 M HEPES PH 7.0. 200 NL PROTEIN + 150 NL ...Details: THE CONCENTRATION OF HB-EGCG ADDUCT WAS 16 MG/ML IN 10 MM TRIS PH 8.0. THE CRYSTALLIZATION RESERVOIR WAS 20% PEG3350, 0.1 M RACEMIC MALIC ACID, 0.05 M HEPES PH 7.0. 200 NL PROTEIN + 150 NL RESERVOIR. SET BY MOSQUITO IN MRC SD2 PLATES, 50 MICROLITER RESERVOIRS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 1.995→48.31 Å / Num. obs: 40813 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.192 / Rrim(I) all: 0.2 / Net I/σ(I): 8.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.052.30329610.8112.3941
2.05-2.111.79728710.871.8651
2.11-2.171.45428000.9251.511
2.17-2.241.07527330.971.1171
2.24-2.311.01726560.971.0571
2.31-2.390.74725730.9850.7781
2.39-2.480.64224810.9830.6681
2.48-2.580.50823850.9880.531
2.58-2.70.41522810.9920.4311
2.7-2.830.34722200.9930.3611
2.83-2.980.28420880.9940.2951
2.98-3.160.2119900.9960.2191
3.16-3.380.17518810.9970.1831
3.38-3.650.1317390.9970.1361
3.65-40.10816170.9970.1131
4-4.470.09714850.9970.1011
4.47-5.160.09413070.9980.0981
5.16-6.320.09511290.9970.0991
6.32-8.940.0748840.9980.0771
8.94-48.310.065220.9970.0631

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEVERSION Jan 10, 2022 BUILT=20220820data scaling
XDSVERSION Jan 10, 2022 BUILT=20220820data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→39.58 Å / SU ML: 0.2994 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 2014 4.93 %
Rwork0.1963 38799 -
obs0.1985 40813 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.11 Å2
Refinement stepCycle: LAST / Resolution: 1.995→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 243 368 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824898
X-RAY DIFFRACTIONf_angle_d0.84556744
X-RAY DIFFRACTIONf_chiral_restr0.044734
X-RAY DIFFRACTIONf_plane_restr0.0086933
X-RAY DIFFRACTIONf_dihedral_angle_d11.42961860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.040.44991400.39072672X-RAY DIFFRACTION97.3
2.04-2.10.39171540.31582728X-RAY DIFFRACTION99.72
2.1-2.160.38211280.29042766X-RAY DIFFRACTION99.76
2.16-2.230.281580.24462705X-RAY DIFFRACTION99.55
2.23-2.310.26571270.23982747X-RAY DIFFRACTION99.52
2.31-2.40.24581410.21972746X-RAY DIFFRACTION99.41
2.4-2.510.27331630.21212744X-RAY DIFFRACTION99.76
2.51-2.650.26881030.19692798X-RAY DIFFRACTION99.38
2.65-2.810.24741940.18982705X-RAY DIFFRACTION99.62
2.81-3.030.22961090.20282809X-RAY DIFFRACTION99.59
3.03-3.330.27141580.20062763X-RAY DIFFRACTION99.46
3.33-3.810.23491430.16882822X-RAY DIFFRACTION99.76
3.82-4.80.1577980.14432872X-RAY DIFFRACTION99.76
4.81-39.580.19111980.17922922X-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)
18.352406782383.582769039150.373920886942.80430355279-1.508388490252.377733972880.1561047421750.33032442090.975791906253-0.847960605701-0.0851134087117-0.0079553591042-0.5374690064120.398120592607-0.074182785020.487027671628-0.06538972926730.1060410251360.5514982589730.008097776446310.458881866994-5.7828.604-45.106
23.5717960263-0.236985048453-0.08518355679593.304530391120.2854885891024.09310774515-0.02669542856860.147600940996-0.304831961528-0.2205477982350.127552983411-0.3109601426920.06975183379850.143344584585-0.03151422803670.257498971466-0.01697242726010.02954549193250.218755788602-0.02971496956020.462094092165-15.319-3.397-29.808
35.078985399221.69911662806-1.792418482924.41812512824-2.128173168324.00717122966-0.06804122661430.467468861751-0.253031655502-0.313122264624-0.006064005996130.2380172823170.10357714650.03168417406610.0519299089170.28812938016-0.0221765596139-0.02226592047560.32145325656-0.1120136419630.462544094235-20.635-2.074-39.694
43.94009179601-0.7157843580540.03585816598193.690995619430.1552196360992.74359575761-0.006254665733810.1343591287870.024710557132-0.135097325965-0.02011175967230.205993839439-0.158926023339-0.02937098954810.01557080231830.244943044938-0.02205050022990.0351610587940.200441654228-0.05011043264720.353537778033-13.9466.449-34.485
52.387359445560.745304944944-0.5005148956393.90064868432-2.387173881222.99635784861-0.0214480316020.1168102043940.1102268884640.0360625838726-0.0156265513272-0.1973579805-0.0321435276571-0.02213632409740.05467496205140.224536005870.00995751894392-0.04645428829840.221537208137-0.03940578244790.4635797503-1.33613.074-21.838
64.953159332943.63787876689-3.493036330436.1275532091-4.433848504877.742865921610.183476098132-0.1518851323980.1066894929420.377980962658-0.426109385062-0.640110829715-0.5693057680250.2457586784490.2356461902830.357139747572-0.0190846476244-0.08399851382630.289844029726-0.05536273684950.6984381683412.80715.723-16.227
75.91234671682-2.060535783491.166360524344.51590489413-4.412566334384.46086404089-0.136952532758-1.159690743110.6341556526081.241704379710.0383099240117-0.045562084741-0.818448101682-0.0986549746772-0.06596630957790.531052781355-0.01580155148550.05230012096590.664947211875-0.1132916473540.680601492381-8.2818.427-7.255
84.60126157976-1.909461319050.5924217929698.473643780290.529289591133.2442383279-0.04373139055620.003813715506170.06924187993210.07622036433420.06633471417430.591950638486-0.0982977899656-0.106473360014-0.01959837438650.221428480518-0.01739609402650.03354174444140.2426606744040.0224484923830.472435793879-6.94312.071-22.439
92.32335982223-1.0043903726-0.6611422895797.751065294255.570951858055.54499460068-0.0146016522329-0.0242752565902-0.0813087336240.05303334528660.0384923606509-0.1064710022760.145285247847-0.126450171823-0.04070267350260.243951914762-0.001500063063010.007214368459580.2359018148740.02148373190540.450222726148-10.5495.385-16.449
102.617365524730.177218450506-2.427627195888.874620611995.918381980736.43260968057-0.960834642440.430021191880.566016008244-0.9884739963781.657173579520.817399894497-0.159093835561-0.650953490759-0.7343814539121.03355116432-0.295233755608-0.3504188662540.8704076862770.1303390634961.20942016282-16.76423.278-10.893
115.434859011984.704152705692.893383788935.154043605445.219411328558.43373671189-0.06982755025840.2842511687320.0694587406037-0.455866329277-0.20909102474-0.251188677154-0.1205832430050.06026417042750.3622915946540.281155325650.0497380213902-0.03287816330770.3602117609940.08900597565830.460037007044-34.32230.088-43.683
123.45972766710.25414112804-0.2497617939631.361048968030.2661456008242.93265877903-0.1176042400070.05067014421560.5706961597770.04823113469520.0691244257967-0.153547976364-0.1652411472980.01876848454290.0710862695270.261497360143-0.010135923981-0.0405887838650.2321831750150.02618503242980.55858868495-22.2538.042-27.41
134.206473714323.339681950073.742064172555.032719272813.463599712855.644755122-0.2034681626620.4026038083690.535111737292-0.4447124826140.173825311662-0.0552479152532-0.501279746170.1545311268050.07035630886270.2474077097090.00160547701299-0.007420189303430.338959405020.1047730017370.608857079298-21.43439.727-37.847
147.23917394257-1.172023867762.799761197075.10565658599-2.211593216688.32839622676-0.0258699137261.06057413426-0.318494043146-0.875200878232-0.509847537552-1.161348415580.3279591327851.254648518250.5251144162870.3882427713670.0512442391680.1373004909860.5116497425210.03199186111880.542606257391-11.52230.063-40
152.6462661585-2.597277188570.3187277470942.65244083979-0.06175191216440.987625125470.03430877460880.1845311081410.02561573212480.0238851782089-0.06608029705230.153963313575-0.04228573149630.01431758093470.08549062071520.2163964535250.0172466469748-0.005801025302540.2396731203530.01979201966750.481097502795-27.24731.367-30.354
167.134428057931.34656637932-1.674230062791.760174848511.396131521353.02166167448-0.3058752254280.0208619126878-0.9431159902860.05979323267090.147032584287-0.08834549799950.2281971039510.2024492714950.1156129806640.2861346590190.0397225286802-0.02318947743850.3035815683990.02092155933390.430098028241-30.80926.262-37.289
178.8757026592.936417571022.461257660565.053657417632.035199019134.006377940230.177379443259-0.6207353671560.949774050090.312165942827-0.0858159659238-0.382048555195-0.1894277488170.136468017855-0.08328227317220.325554051361-0.001595420366050.05646343809550.341357497482-0.08965481316640.585835000338-34.37933.86-10.32
183.4328190733-0.0656762029268-1.664009185642.49402401708-0.2849695472763.2022843925-0.04783803685890.327253612534-0.326547219183-0.106248125008-0.04183869858770.2653061020270.2036593516-0.0883156023610.08214796520680.2337304612920.00152699431173-0.04739776596390.254466394970.01133386935190.497043220019-41.1315.259-28.375
197.083052269094.283966958224.735752203887.280657254325.766466552868.83674267711-0.0685626726231-0.1077101597070.07452063557770.676461369981-0.09586814160020.8318714518360.646617567214-0.1028252171650.2497265835550.3544811884410.02906101296610.06878284856980.2504732964880.04994017810360.574964483009-42.75419.532-15.709
205.032973844680.4624809123990.3226786370929.201809024194.387604010466.93603924149-0.166446684139-1.51297042999-0.6956566271111.765638596320.471114861219-0.5778921898030.6622539923860.138504462703-0.3315097858330.5161492731360.0230955549128-0.1432453700960.6973784015530.2535295317180.529722649875-31.55415.307-7.504
217.166606985320.976327182032-1.137780700621.22168805173-0.5171087111792.08350889386-0.759047096205-0.758521564368-1.336050436430.4251016364980.7782189287020.5743615689171.788576016880.0851285464838-0.01863237776740.6859738019870.02402374781590.09025139547340.4784913076940.1506185088990.968905384793-30.4076.395-18.755
222.90426856229-1.928830283450.1471913765412.106124213-1.11110962732.36956649703-0.05737277850750.03709876331290.4164232429790.3039172829640.0213420506107-0.231501237422-0.146356600866-0.09658024473140.06255249074130.197691110491-0.0222709204839-0.02954032284480.248198880679-0.003475949865910.519860686015-34.1826.85-23.187
234.8827285422-1.853479027461.242465850497.96988386218-5.671772814846.93736967838-0.052059504549-0.4541098654770.5619463494380.09044985207820.196600900892-0.2333538842670.0919215544167-0.179727601558-0.1412956187010.218239550569-0.0236032757913-0.0439427831060.248272603717-0.05014346284730.38763808156-29.3729.063-16.134
243.50128135656-1.994967849990.07710886872084.25281468579-5.783789872332.002115934130.023009159438-0.679690480768-0.675210383019-0.592147889321.026652500590.7107240533041.549788859340.41966383637-0.9953871758941.20505532399-0.104077273111-0.2247680541920.70197945155-0.01535032241851.147270623-23.53511.567-11.154
253.78713364385-1.29782119735-2.516031467253.13556485931-0.5672215144094.19065394992-0.08603517356210.909494763928-0.846063182455-0.4270787022360.128092861088-0.01194215652360.690579647445-0.198178483434-0.0555770832080.41870173738-0.01843094920880.0196643662670.228378927648-0.1333260150660.0366885163275-24-0.952-36.326
265.63334379035-0.1255900017275.473379873181.8837183224-0.6889741550785.50313193656-0.589845293641-0.1149346978261.463263310020.4826444104980.0499931162759-0.411504179026-0.2803999057730.495677315540.5679557490290.39875595129-0.0357683010037-0.06659851923390.363663153811-0.0141258535960.53983731372-2.64921.99-17.024
277.84907806299-4.054366877974.643192434343.25691131429-1.903310326433.20215732458-0.2641733122260.30877016840.591012160630.0602963925170.0215108676867-0.500861376124-1.02182075940.456864166570.239614494590.329299114508-0.0432249132492-0.06048964278160.3069156194920.03672777890150.613337928295-16.03336.062-36.036
283.737567525682.19885372628-1.231837248324.090272403472.33674999023.76954799830.188720898715-0.0119407034961-1.16157942060.380386255549-0.2044848454880.1758397957710.620650931142-0.524653153956-0.07666859750910.419093774315-0.0421113144819-0.02766643430520.3413634561630.009043312449350.46703181113-37.42512.9-17.386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:15 )A1 - 15
2X-RAY DIFFRACTION2( CHAIN A AND RESID 16:42 )A16 - 42
3X-RAY DIFFRACTION3( CHAIN A AND RESID 43:88 )A43 - 88
4X-RAY DIFFRACTION4( CHAIN A AND RESID 89:138 )A89 - 138
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:57 )B1 - 57
6X-RAY DIFFRACTION6( CHAIN B AND RESID 58:75 )B58 - 75
7X-RAY DIFFRACTION7( CHAIN B AND RESID 76:94 )B76 - 94
8X-RAY DIFFRACTION8( CHAIN B AND RESID 95:121 )B95 - 121
9X-RAY DIFFRACTION9( CHAIN B AND RESID 122:141 )B122 - 141
10X-RAY DIFFRACTION10( CHAIN B AND RESID 142:146 )B142 - 146
11X-RAY DIFFRACTION11( CHAIN C AND RESID 1:20 )C1 - 20
12X-RAY DIFFRACTION12( CHAIN C AND RESID 21:43 )C21 - 43
13X-RAY DIFFRACTION13( CHAIN C AND RESID 44:75 )C44 - 75
14X-RAY DIFFRACTION14( CHAIN C AND RESID 76:94 )C76 - 94
15X-RAY DIFFRACTION15( CHAIN C AND RESID 95:112 )C95 - 112
16X-RAY DIFFRACTION16( CHAIN C AND RESID 113:138 )C113 - 138
17X-RAY DIFFRACTION17( CHAIN D AND RESID 1:19 )D1 - 19
18X-RAY DIFFRACTION18( CHAIN D AND RESID 20:57 )D20 - 57
19X-RAY DIFFRACTION19( CHAIN D AND RESID 58:76 )D58 - 76
20X-RAY DIFFRACTION20( CHAIN D AND RESID 77:94 )D77 - 94
21X-RAY DIFFRACTION21( CHAIN D AND RESID 95:99 )D95 - 99
22X-RAY DIFFRACTION22( CHAIN D AND RESID 100:121 )D100 - 121
23X-RAY DIFFRACTION23( CHAIN D AND RESID 122:141 )D122 - 141
24X-RAY DIFFRACTION24( CHAIN D AND RESID 142:146 )D142 - 146
25X-RAY DIFFRACTION25( CHAIN A AND ( RESID 201:201 OR RESID 309:309 ) )A201
26X-RAY DIFFRACTION25( CHAIN A AND ( RESID 201:201 OR RESID 309:309 ) )A309
27X-RAY DIFFRACTION26( CHAIN B AND ( RESID 201:201 OR RESID 305:305 ) )B201
28X-RAY DIFFRACTION26( CHAIN B AND ( RESID 201:201 OR RESID 305:305 ) )B305
29X-RAY DIFFRACTION27( CHAIN C AND ( RESID 201:201 OR RESID 301:301 ) )C201
30X-RAY DIFFRACTION27( CHAIN C AND ( RESID 201:201 OR RESID 301:301 ) )C301
31X-RAY DIFFRACTION28( CHAIN D AND ( RESID 201:201 OR RESID 302:302 ) )D201
32X-RAY DIFFRACTION28( CHAIN D AND ( RESID 201:201 OR RESID 302:302 ) )D302

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