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- PDB-7lbw: Crystal structure of TFAM (mitochondrial transcription factor A) ... -

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Basic information

Entry
Database: PDB / ID: 7lbw
TitleCrystal structure of TFAM (mitochondrial transcription factor A) bridging two non-sequence specific DNA substrates
Components
  • (DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)- ...) x 2
  • Transcription factor A, mitochondrial
KeywordsTRANSCRIPTION/DNA / Mitochondrial transcription / transcription initiation / mtDNA / promoter recognition / DNA bending / HMG box / mtDNA packaging / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / mitochondrial transcription / DNA binding, bending / mitochondrial nucleoid / heat shock protein binding / response to nutrient ...Mitochondrial transcription initiation / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / mitochondrial transcription / DNA binding, bending / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Mitochondrial protein degradation / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / mitochondrion / RNA binding / nucleus / cytosol
Similarity search - Function
: / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Transcription factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsChoi, W.S. / Garcia-Diaz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM).
Authors: Choi, W.S. / Garcia-Diaz, M.
History
DepositionJan 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 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 1.2Oct 18, 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: Transcription factor A, mitochondrial
B: Transcription factor A, mitochondrial
C: DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)-3')
D: DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)-3')
E: DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)-3')
F: DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,59315
Polymers75,9026
Non-polymers6919
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.000, 124.810, 55.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 45 through 61 or (resid 62...
d_2ens_1(chain "B" and (resid 45 through 75 or resid 77...
d_1ens_2chain "C"
d_2ens_2(chain "E" and (resid 1 through 18 or (resid 19...
d_1ens_3chain "D"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALALAA2 - 32
d_12ens_1THRPHEA34 - 74
d_13ens_1GLUILEA76 - 90
d_14ens_1ASPPHEA92 - 127
d_15ens_1GLULEUA129 - 139
d_16ens_1THRGLUA141 - 177
d_17ens_1METILEA180 - 181
d_18ens_1VALARGA183 - 191
d_21ens_1VALALAB2 - 32
d_22ens_1THRPHEB34 - 74
d_23ens_1GLUILEB76 - 90
d_24ens_1ASPPHEB92 - 127
d_25ens_1GLULEUB129 - 139
d_26ens_1THRGLUB141 - 177
d_27ens_1METILEB179 - 180
d_28ens_1VALARGB182 - 190
d_11ens_2DTDGC
d_21ens_2DTDGE
d_11ens_3DCDAD
d_21ens_3DCDAF

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.997855023516, -0.0194316913219, 0.0625120901608), (-0.00764480913274, -0.913803748405, -0.406084063089), (0.0650146824743, -0.405690915321, 0.911695109282)-39.8060102149, 48.9691810944, 11.1326224646
2given(-0.995941653846, -0.00962375203601, 0.0894852252098), (-0.027638962246, -0.913518265297, -0.405857692712), (0.0856522615, -0.406683860467, 0.90954490144)-40.1799019007, 48.7607687132, 11.9604789998
3given(-0.994324401562, -0.0244318977655, 0.103547413441), (-0.0186192802732, -0.918292868524, -0.395463689888), (0.104748779758, -0.3951471751, 0.912626102602)-39.4160470775, 48.9443657428, 12.9003203153

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcription factor A, mitochondrial / mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / ...mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / Transcription factor 6-like 2


Mass: 24450.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFAM, TCF6, TCF6L2 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3) / References: UniProt: Q00059

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DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)- ... , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)-3')


Mass: 6683.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G)-3')


Mass: 6817.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 232 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris (pH 6.5) and 24% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.84→39.81 Å / Num. obs: 19494 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 73.13 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 33.6
Reflection shellResolution: 2.84→2.85 Å / Rmerge(I) obs: 0.636 / Num. unique obs: 179

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TQ6

3tq6


Resolution: 2.84→39.81 Å / SU ML: 0.3027 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.39
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 996 5.12 %
Rwork0.1987 18446 -
obs0.2004 19442 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.58 Å2
Refinement stepCycle: LAST / Resolution: 2.84→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 1767 45 223 5249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325305
X-RAY DIFFRACTIONf_angle_d1.42057469
X-RAY DIFFRACTIONf_chiral_restr0.0743806
X-RAY DIFFRACTIONf_plane_restr0.0238649
X-RAY DIFFRACTIONf_dihedral_angle_d26.19762217
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.46520421607
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.580291890485
ens_3d_2DX-RAY DIFFRACTIONTorsion NCS0.579135347464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.990.37931210.29182568X-RAY DIFFRACTION99.81
2.99-3.170.32381490.26372593X-RAY DIFFRACTION99.96
3.17-3.420.28091480.22362592X-RAY DIFFRACTION99.93
3.42-3.760.25851500.20142602X-RAY DIFFRACTION100
3.76-4.310.19121250.19122659X-RAY DIFFRACTION99.96
4.31-5.420.20361440.18252649X-RAY DIFFRACTION100
5.43-39.810.21431590.18012783X-RAY DIFFRACTION99.83
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)
10.1658664487520.1422736956620.09825866523830.09004345448940.06641146518280.04307501772460.0134657039943-0.714362481495-0.2082851898780.3714440738210.2488725201680.112755556892-0.2252997694980.147352887363-3.46640299291E-60.5232677904650.03086242521460.05267615903690.7839414083620.00680924245590.450681002542-37.81424.343-28.973
20.3706364577740.2718675393380.08289574789680.1864516817950.1123826385990.5194822530760.141657201209-0.307062539739-0.816338511518-0.0358248878574-0.9876606524931.07315703588-0.377777129774-0.3401064352160.004152080454460.5391632931330.07207879235310.02324665692671.02662030831-0.06194974413880.885767332449-55.64621.35-15.922
31.582931657240.9257317292350.6785191299921.251054928721.05503533741.408523765370.01682871442960.1232382854410.1559271723570.07694382507440.1588829144390.282623035152-0.167825368279-0.0714171310757-3.17933854321E-60.5757871607120.01474808168590.1086048065130.5351827307020.1157525385280.461913908874-30.8237.264-10.554
40.1576901093140.1222684038190.1096655655730.04332437132230.08375425468960.0438836814504-0.253241397546-0.351494932575-0.122910027996-0.3185748858750.03106521983830.258961356023-0.3016997981350.151988320599-1.10848012097E-50.371256060613-0.04199642303250.06303969290450.460956524435-0.0105983970670.627435646329-4.17337.968-27.549
50.119124575318-0.286131843091-0.07736256509841.11395726454-0.326151038170.4625722605780.748890364904-0.377035522227-0.130971075961-0.643148232229-0.360441147899-0.6396790242530.286323815490.2041934194550.01095960133390.4860625505040.0908573911944-0.08677368210230.795081413323-0.05039089805170.59247765650114.0836.551-15.076
60.3586700631660.0539108528737-0.2946778767150.108580453808-0.2899345725851.03297088751-0.0995373667187-1.12858796013-0.3249472425791.18451410683-0.0593305835663-1.902179687980.11814746860.666280575591-0.01603682560010.5169506870090.0647494206547-0.1414081623650.7140716596280.01282765019710.80624125111513.8634.725-7.15
70.967029941885-0.1731990947160.3266375456691.72480153462-0.1076803962010.137636482919-1.02885524260.1776417581361.68520533699-0.280868403516-0.09809051905040.454725707178-0.681620155580.0754228716655-0.0115510546810.436988303382-0.065630051503-0.04217003605480.517508409206-0.02905994500760.552825253175-0.16548.367-25.281
81.371572017190.7209533881990.4498242722272.024264119190.4700570108862.219654175540.0008624286065120.161097033713-0.6019490261740.519633374845-0.111487703881-0.2119877899720.971662713397-0.147690688292-0.002424493334541.04785491775-0.07164349301230.06566718284830.461816852024-0.08630629832460.735089240113-17.3788.611-14.934
90.02467585556940.08740987066510.06312697053380.1743443133940.1638838914870.1214923987170.1992562437660.5392461627780.0296877818981-0.447066189583-0.6211885677510.8457829292531.091662926950.75843805925.2925047402E-71.07253133033-0.303512800269-0.06646861442471.203232376780.3876388416171.03735954095-30.97847.092-15.92
100.1516688891310.254916516194-0.02030717815980.374009016868-0.024674821263-0.01020502802290.2086006790561.135574866720.692078642987-0.9815033054310.127097678432-0.1611189547010.0125306891274-0.216608943902-6.704267083380.7741740359090.03745738430690.08663212462830.7712335227450.1708431217410.840289341465-17.42154.066-10.28
110.08684920799050.162572871964-0.1047401599140.244069124466-0.1624693041810.123779424483-0.3187595668450.88749658361-0.3361715635540.2007800097930.606503297837-1.081337125241.26321310765-0.2178913137220.03140646187570.6179540248180.03217578453580.1061062860970.823580403349-0.2691287062940.772682444681-7.92338.081-11.651
120.01870409616710.0306072581572-0.03274953085480.0412630802696-0.03996315571320.00854995027643-0.3063383414010.564095931387-2.09506552421-0.207360646909-0.1817815257780.1973125138061.991577557740.460393044416-0.1296569313771.101942157940.2063449284580.1773837589360.550438834411-0.06655501027251.179704828526.90626.113-16.507
130.02049254569510.01180126893780.0153164552330.0246726296324-0.0139335600550.0310208282776-0.730643782354-0.778987895528-0.507057388673-0.1568524476520.2057437914420.0437910259290.118693759062-0.3625237450252.88161930678E-51.15586477729-0.146755139451-0.2771821605690.8548943091750.102635930381.88511205509-0.3715.084-13.108
140.11763420805-0.00339516854614-0.04420519281170.00588375894229-0.01554352234050.01174129482710.7823081226260.766086912092-1.71086491157-1.660785706980.7288856688260.8920121567860.6888535518380.6748004690813.44218939627E-51.42910833206-0.1936897178380.08827299044281.3026567599-0.1141720737721.19842295879-40.05333.171-11.498
151.081803245421.07988618767-0.8242271046351.55972749823-0.4608338625180.9249486572520.478842166885-1.713265822730.7986923166931.08423347231-1.11177053174-0.948364178614-0.6520146985270.9085721927-0.05184728950620.8525716119080.118840798749-0.04116140703521.378529507250.1002241112610.923534606549-44.00416.841-11.43
161.10330389171-0.4015497643250.4743402976550.258032820899-0.2361050835790.213621904792-0.5807898655481.240707328621.272267688930.1520130868760.521073770175-0.252751110636-1.17432572686-1.11533918834-0.007942267439670.6465485182610.1053714634140.01055268674091.510344646850.05311285215851.01450039999-26.90314.014-19.655
170.008138484335660.03864146689-0.05413865236910.0536232993495-0.1206784232240.189689777307-0.8431547348151.07527748404-0.6344770877030.389505490820.126433832533-1.33981304717-0.3530105791680.338861209753-3.06753686741E-60.93436182252-0.006401413878750.1954900077740.970328043841-0.2138712362331.37850665227-10.4554.491-20.273
180.0053811426053-0.0062844700254-0.01074153486950.02076574143950.01741525770760.03231288580840.6659769397120.6359354174610.388587237769-0.652431901966-0.732160060938-0.439200700936-0.06642910686690.764597182154-2.676671376580.879489203686-0.1355737987030.3508810473421.13832827754-0.2988972145781.7838968258-1.9913.328-27.127
190.08756935320390.0400602474490.168990665230.2471470415060.1405505698770.265448582476-0.5264360453391.245622632330.307321381348-0.3370701862270.2028370939330.400512155633-0.752904072093-0.828779816841.0402436803E-60.991118318497-0.150021860887-0.04893083007011.1269697356-0.2497389725161.07469287059-17.8928.722-22.6
200.1044363072250.1992198364280.2049725561780.338760629460.5141846046870.5038133501390.340474780776-0.3850990867530.8470140612420.142063385424-0.2203389559010.157179803081-0.5340682487590.424252709554-3.94280568932E-71.030377710880.1208141791210.01074766982950.9317575751570.03502515942991.42808188732-40.92427.556-12.587
211.248108940070.9329526979760.7269974289761.02223452835-0.08221697970040.5598726329170.402288146296-0.548603464261-0.946300909902-0.641254594895-0.1529690387410.2335451224720.544364436865-1.08543316429-0.0339825829560.8361984580860.00503453436588-0.031354169110.5832970681930.00172666091740.8084999000350.50831.45-11.667
220.2726387292380.386331373736-0.2300502823182.680123337380.09852274927430.304402496302-0.3716780401041.2356409690.07402179796620.0810226151340.4631059135320.8630705551830.249348020235-0.7118518000848.48685354832E-50.512005362330.02100589305590.0402525501740.9148781479020.1932381224740.839721149509-25.89148.519-12.043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:55 )A44 - 55
2X-RAY DIFFRACTION2( CHAIN A AND RESID 56:71 )A56 - 71
3X-RAY DIFFRACTION3( CHAIN A AND RESID 72:236 )A72 - 236
4X-RAY DIFFRACTION4( CHAIN B AND RESID 44:55 )B44 - 55
5X-RAY DIFFRACTION5( CHAIN B AND RESID 56:71 )B56 - 71
6X-RAY DIFFRACTION6( CHAIN B AND RESID 72:92 )B72 - 92
7X-RAY DIFFRACTION7( CHAIN B AND RESID 93:122 )B93 - 122
8X-RAY DIFFRACTION8( CHAIN B AND RESID 123:233 )B123 - 233
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:5 )C1 - 5
10X-RAY DIFFRACTION10( CHAIN C AND RESID 6:10 )C6 - 10
11X-RAY DIFFRACTION11( CHAIN C AND RESID 11:15 )C11 - 15
12X-RAY DIFFRACTION12( CHAIN C AND RESID 16:20 )C16 - 20
13X-RAY DIFFRACTION13( CHAIN C AND RESID 21:22 )C21 - 22
14X-RAY DIFFRACTION14( CHAIN D AND RESID 1:5 )D1 - 5
15X-RAY DIFFRACTION15( CHAIN D AND RESID 6:10 )D6 - 10
16X-RAY DIFFRACTION16( CHAIN D AND RESID 11:15 )D11 - 15
17X-RAY DIFFRACTION17( CHAIN D AND RESID 16:20 )D16 - 20
18X-RAY DIFFRACTION18( CHAIN D AND RESID 21:22 )D21 - 22
19X-RAY DIFFRACTION19( CHAIN E AND RESID 1:10 )E1 - 10
20X-RAY DIFFRACTION20( CHAIN E AND RESID 11:22 )E11 - 22
21X-RAY DIFFRACTION21( CHAIN F AND RESID 1:10 )F1 - 10
22X-RAY DIFFRACTION22( CHAIN F AND RESID 11:22 )F11 - 22

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