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

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Basic information

Entry
Database: PDB / ID: 7lbx
TitleCrystal structure of TFAM (mitochondrial transcription factor A) in complex with LSP
Components
  • DNA (5'-D(P*TP*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*AP*A)-3')
  • 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 promoter sequence-specific DNA binding / mitochondrial transcription factor activity / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / mitochondrial transcription / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Transcriptional activation of mitochondrial biogenesis ...Mitochondrial transcription initiation / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription factor activity / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / mitochondrial transcription / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / 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
DNA / DNA (> 10) / Transcription factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*TP*AP*A)-3')
D: DNA (5'-D(P*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*AP*A)-3')
E: DNA (5'-D(P*TP*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*TP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,26513
Polymers75,9066
Non-polymers3597
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.425, 120.507, 55.236
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_1chain "C"
d_2ens_1chain "E"
d_1ens_2chain "D"
d_2ens_2chain "F"
d_1ens_3(chain "A" and (resid 44 through 54 or resid 56...
d_2ens_3(chain "B" and (resid 44 through 54 or resid 56...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1DTDAC
d_21ens_1DTDAE
d_11ens_2DTDAD
d_21ens_2DTDAF
d_11ens_3SERVALA1 - 11
d_12ens_3SERLYSA14 - 20
d_13ens_3GLNLYSA22 - 105
d_14ens_3LEUARGA108 - 191
d_21ens_3SERVALB1 - 11
d_22ens_3SERLYSB13 - 19
d_23ens_3GLNLYSB22 - 105
d_24ens_3LEUARGB107 - 190

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.991325526492, 0.03690412698, -0.126141927749), (0.0201137202219, -0.905864419361, -0.423089933695), (-0.129881248775, -0.421957034717, 0.897264243169)-38.3505676588, -45.8027435248, -12.9013044837
2given(-0.988728669791, 0.0278578130094, -0.147103908135), (0.0404644893795, -0.896249313722, -0.441701021905), (-0.144146601186, -0.442674948361, 0.885020139579)-38.4626446883, -44.354102637, -13.7355155947
3given(-0.990703278612, 0.0326654661008, -0.132060520491), (0.0265465597345, -0.905662710042, -0.423167030622), (-0.133425237171, -0.422738717134, 0.896375860408)-37.4667667568, -45.2755312995, -13.0930521913

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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 chain , 2 types, 4 molecules CEDF

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


Mass: 6609.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*AP*A)-3')


Mass: 6893.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 182 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES (pH 7.5), 0.05 M MgCl2, and 32.5% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→82.6 Å / Num. obs: 21463 / % possible obs: 99.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 66.5 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.4
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.884 / Num. unique obs: 987

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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: 2.7→29.12 Å / SU ML: 0.3564 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 1012 4.72 %
Rwork0.2083 20451 -
obs0.2099 21463 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.69 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 1788 22 175 5174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01285297
X-RAY DIFFRACTIONf_angle_d1.34687488
X-RAY DIFFRACTIONf_chiral_restr0.0786802
X-RAY DIFFRACTIONf_plane_restr0.0124649
X-RAY DIFFRACTIONf_dihedral_angle_d26.8982205
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.858184951289
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.739284344095
ens_3d_2AX-RAY DIFFRACTIONTorsion NCS2.6091935774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.31631340.29732872X-RAY DIFFRACTION99.67
2.84-3.020.30531300.28112889X-RAY DIFFRACTION99.8
3.02-3.250.31641400.2692898X-RAY DIFFRACTION99.67
3.25-3.580.25041270.21972879X-RAY DIFFRACTION99.73
3.58-4.090.21751530.20332904X-RAY DIFFRACTION99.97
4.1-5.150.22421480.18272962X-RAY DIFFRACTION99.94
5.16-29.120.22911800.18433047X-RAY DIFFRACTION99.51
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)
10.539182888963-0.235372779874-0.7749882893850.779494705671.160875824261.738282643210.2900132795060.827692842267-0.959623184646-0.2749255799240.05337023333520.855971002298-0.01446910088720.273363191430.0009744533843930.603135394435-0.0853844785059-0.1093883031610.688960105055-0.1562300815521.0319176831-49.666-21.95518.57
21.113432600890.208158916783-0.2085653463740.46079371428-0.1267978602210.0598600399899-0.1329380262461.58782104743-1.30363731026-1.90917325491-0.2227151349540.898509793072-1.22110298225-0.179104241746-0.05290048249461.328709226440.33725937088-0.3116929906121.17194676197-0.2609253874780.539379729228-54.169-15.5118.092
32.31709101128-2.25045751054-0.4619505466440.7264254851830.6478052964891.68193667910.042460513835-0.1574966600490.238481427251-0.174531742810.13289938767-0.0691910611495-0.08215712439210.2976894090257.14232557848E-80.70558190001-0.07381554323760.02518960045340.687352436036-0.02530382712070.613407136181-34.461-20.62824.298
41.2276609265-0.6216841054180.08479030496750.8126902619450.4680581156120.400208347988-0.367270144611-0.975628592151-0.80684332951-0.3261417915780.6004634655930.5049669798560.153094135666-1.283968576080.00326390880570.7392944095050.0227097753145-0.1581345662920.5201035304070.0113882254080.404790094709-22.911-43.327-0.665
55.33821402833-3.5290798096-6.330019345664.270594473523.85513244937.567282200990.09004405295130.564243028503-0.628270228905-0.740111946414-0.7484677712380.7635573057661.39879817907-1.46001308333-1.249703281520.92233623434-0.270744486137-0.4622806277690.4982136837250.2443898468480.80779535757-26.106-58.8883.341
61.615723613380.9984763756741.854715393430.6348404705771.160623667872.14417742024-0.8865663437831.71538409653-0.9022924814110.0740599865139-1.029941494061.52334402744-1.11646908015-0.125659455159-0.4543849636811.05356507043-0.957109404447-0.5424142276191.078756831050.2230647995861.46606531348-36.096-61.8910.326
71.32757718775-1.46176953125-1.095330287463.674905577241.870995608392.191293443320.213105964443-0.911984281953-1.205333967481.020443132150.1896437424291.550246714541.80677834793-0.2253039895050.06610848800461.269210733-0.577605416662-0.4308595430620.918746208450.564766186250.671066497371-26.959-62.51611.895
82.292797270271.184653877631.188073425390.6772661441781.027760007453.965411150560.4024313846560.170235211825-0.296620325555-1.11608615315-0.1862355437960.3824413331960.4187337741080.0888257734631-3.27161161681E-70.8818130020030.0179178360964-0.1717030763050.6454586849760.05277982850880.521229398228-18.519-48.061-5.549
90.6263407864340.121306776128-0.8603570435984.71687627363-2.321971763282.2364586833-0.083151297006-0.1364751295241.022454198150.174887570164-0.658834044914-1.37827073601-2.542900248020.519549519787-0.7378190079431.520746791030.00670424333294-0.269535728530.394536220992-0.02762364827040.611239935585-16.083-29.263-2.031
102.30873002481-1.16028145294-0.09444604115262.057123356680.6743998067461.99652849172-0.186897600906-0.2390679350230.362316238775-0.05671032472140.128797337153-0.132858833555-0.239160920666-0.000704980328136-0.000874317140.595795367419-0.0797923957357-0.03032537790790.557120244246-0.06228000171650.573352824984-3.293-25.88319.828
113.502951337511.07897623346-0.07250605401290.760199838325-0.7024253180891.115293058760.8150493772340.04136269124740.359069880141-0.927810035812-0.494152473548-0.1324799852930.0682145956228-0.2768349715820.01101599134362.173473917410.286173437545-0.510626764180.724008570129-0.03250552091361.26700794863-18.133-3.3033.245
120.246590379850.0327169510178-0.1850574225580.1273900278340.2203914794730.2136691420660.124879351948-0.679919285449-1.31673938782-0.381171116681-0.620465162594-1.50069597102-0.5683482940521.87931052521.14561624831E-50.893331135625-0.3366018258370.2062548709051.26195669130.04340162485391.23742862966-37.239-19.17516.473
130.1942494798660.0165405443296-0.1553475570190.0947143131796-0.1186555537160.1668664582771.505800390761.09720295936-1.20097023344-0.330580451346-0.4551456880810.4944710696551.155459271980.1575730318455.45650415779E-61.192216705220.109616111998-0.1399401108561.08637046049-0.3315540581251.48548206336-47.805-32.04110.275
140.4308901588440.239413381575-0.1474332645040.242552517469-0.05105627066570.04712610637440.3100417944930.673831175914-1.14955363657-1.44085540055-0.688530988880.233980984415-1.83119355122-0.7280066452452.28631541453E-61.441915923040.32271114127-0.01725587717851.2875501488-0.02536887715180.992686533402-32.867-41.71412.252
150.554009398135-0.6745940554140.3808390014191.0542886173-0.231598240570.3726973961620.263858562521-1.81938819202-0.7942527164030.7523405719810.1317644015740.6732965080730.685913045656-0.756548749816-0.003810472746590.72083222599-0.196578031008-0.1949919093490.9776517386880.1971355613310.749230693439-21.227-53.48612.538
160.136361318960.104919031216-0.007294706427590.0797546001221-0.03843854066380.1282507832770.283357426256-0.5950323005230.6166133976350.227524603169-0.661438003368-0.5878532222530.5730637250381.26956218983-0.001591691907890.626220432676-0.202388025846-0.03599224204750.6133267637280.0157899431320.632889692743-12.768-43.8154.694
170.239998073003-0.66257133768-0.1242378651381.7422304754-0.4346354085611.48544806111-0.215259950673-1.25363454762-0.192842624453-0.02670550858970.2772322373140.765437203799-0.553039216785-1.048399895440.0007598969747520.646802230156-0.0692560912665-0.06347893998021.3552973583-0.002198239557940.900670167915-31.522-42.81911.533
181.13996112292-1.013568084090.3869887401551.360275275240.1280224313120.4927145393280.5198686389990.833118467869-0.635406638719-1.11052794073-0.221668508381-0.0473423669289-1.075862094092.091355539580.02553911301971.10213992246-0.239112282286-0.0004047505788681.3041494561-0.02751135420590.820302481156-42.49-15.52511.798
190.0308024934231-0.1150680821660.02939899821990.393835445589-0.0154899196902-0.0271082409974-0.707077269282-2.738595499720.986442192015-0.466214958754-0.03338950417150.230026383013-1.50339162102-1.44428025455-0.008818765924010.588073827314-0.110746989896-0.1297420409611.07508402326-0.1319559266120.895420828866-4.493-36.09115.27
200.160151500843-0.07982745342810.01183456016290.115761244113-0.0663665160858-0.006734850574410.0795346191313-0.1247236554561.65026131111.73776952736-0.318510687583-0.4519147759-1.090591424470.0817738840163-5.57793743586E-60.685967793907-0.0930047386744-0.1115024685480.680303554384-0.1018009296381.366028359086.773-22.07515.464
210.9032012706790.4575034638380.6905490505811.10439658361.072358076361.10323704681-0.338473168687-0.9274488034551.434420373380.255896222757-0.3504316416980.9695294151150.147872058198-0.833935745986.03517435243E-81.05170280141-0.05936753784020.102236400671.15949983957-0.38381284351.34548743359-17.216-8.40820.087
220.201920976289-0.1009703966220.5368427323032.22228002546-0.1736631495191.73025127324-0.0880027440711-0.9368482257731.034150124551.00686478376-0.06669464428150.2802042763140.09206765036-0.4168007710837.10469451516E-50.838878741748-0.0644979361528-0.0435474987620.906904487863-0.2369383172861.21618508752-10.041-12.33619.993
231.7896880479-1.76996849648-1.028861735342.604031045930.6116856329470.8144961802130.3972782031040.3273433138291.110363747530.000430937991702-0.257337132833-2.43720919082-0.357611123927-0.7538474533290.02615809514270.570936548138-0.0635438223549-0.09824988389220.5602631320850.06672795270550.7594411202083.402-34.0837.907
240.366672979706-0.3607486141540.3391796274780.562366786503-0.9349465110411.98616643071-0.67754663210.1088597477330.234904897187-0.731899520041.01528518116-0.4975497081150.641914235591-1.391073998240.02698216336710.533880393994-0.217343544282-0.1441447364820.675641320245-0.03582113349310.680188568504-4.605-45.29214.038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:76 )A44 - 76
2X-RAY DIFFRACTION2( CHAIN A AND RESID 77:92 )A77 - 92
3X-RAY DIFFRACTION3( CHAIN A AND RESID 93:151 )A93 - 151
4X-RAY DIFFRACTION4( CHAIN A AND RESID 152:160 )A152 - 160
5X-RAY DIFFRACTION5( CHAIN A AND RESID 161:169 )A161 - 169
6X-RAY DIFFRACTION6( CHAIN A AND RESID 170:177 )A170 - 177
7X-RAY DIFFRACTION7( CHAIN A AND RESID 178:193 )A178 - 193
8X-RAY DIFFRACTION8( CHAIN A AND RESID 194:224 )A194 - 224
9X-RAY DIFFRACTION9( CHAIN A AND RESID 225:233 )A225 - 233
10X-RAY DIFFRACTION10( CHAIN B AND RESID 44:193 )B44 - 193
11X-RAY DIFFRACTION11( CHAIN B AND RESID 194:232 )B194 - 232
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1:5 )C1 - 5
13X-RAY DIFFRACTION13( CHAIN C AND RESID 6:10 )C6 - 10
14X-RAY DIFFRACTION14( CHAIN C AND RESID 11:15 )C11 - 15
15X-RAY DIFFRACTION15( CHAIN C AND RESID 16:20 )C16 - 20
16X-RAY DIFFRACTION16( CHAIN C AND RESID 21:22 )C21 - 22
17X-RAY DIFFRACTION17( CHAIN D AND RESID 1:15 )D1 - 15
18X-RAY DIFFRACTION18( CHAIN D AND RESID 16:22 )D16 - 22
19X-RAY DIFFRACTION19( CHAIN E AND RESID 1:5 )E1 - 5
20X-RAY DIFFRACTION20( CHAIN E AND RESID 6:10 )E6 - 10
21X-RAY DIFFRACTION21( CHAIN E AND RESID 11:22 )E11 - 22
22X-RAY DIFFRACTION22( CHAIN F AND RESID 1:15 )F1 - 15
23X-RAY DIFFRACTION23( CHAIN F AND RESID 16:20 )F16 - 20
24X-RAY DIFFRACTION24( CHAIN F AND RESID 21:22 )F21 - 22

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