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- PDB-8cle: Vinblastine bound to tubulin (T2R-TTL) complex -

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Basic information

Entry
Database: PDB / ID: 8cle
TitleVinblastine bound to tubulin (T2R-TTL) complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / Drug-tubulin-complex Cell cycle inhibition
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity ...positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-VLB / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWranik, M. / Bertrand, Q. / Kepa, M.W. / Weinert, T. / Steinmetz, M. / Standfuss, J.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.
Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, J.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
B: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,29515
Polymers247,4236
Non-polymers2,8739
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21510 Å2
ΔGint-122 kcal/mol
Surface area81060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.390, 159.740, 182.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACDBEF

#1: Protein Tubulin alpha-1B chain


Mass: 48966.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 48391.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4


Mass: 14207.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Protein Tubulin-Tyrosine Ligase


Mass: 38500.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 41 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-VLB / (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE / VINBLASTINE


Mass: 810.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H58N4O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 6% PEG4000 (w/v), 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.03 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.1→15.13 Å / Num. obs: 56577 / % possible obs: 100 % / Redundancy: 42.8 % / CC1/2: 0.771 / Net I/σ(I): 3.07
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5570 / CC1/2: 0.26
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: Hydroxyethylcellulose / Description: High-viscosity injection / Injector diameter: 75 µm

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Processing

Software
NameVersionClassification
PHENIX1.20_4487refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
PHENIX1.20_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→15.13 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1261 2.46 %
Rwork0.1995 --
obs0.2007 51318 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→15.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 183 32 17471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.995
X-RAY DIFFRACTIONf_dihedral_angle_d10.6532479
X-RAY DIFFRACTIONf_chiral_restr0.0612686
X-RAY DIFFRACTIONf_plane_restr0.0063168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.33281380.3025490X-RAY DIFFRACTION100
3.33-3.480.34771390.2655484X-RAY DIFFRACTION100
3.48-3.660.2791390.23795504X-RAY DIFFRACTION100
3.66-3.880.27041390.2135537X-RAY DIFFRACTION100
3.88-4.180.26161400.18685543X-RAY DIFFRACTION100
4.18-4.590.21461400.17255562X-RAY DIFFRACTION100
4.59-5.230.21281390.16595568X-RAY DIFFRACTION100
5.23-6.50.24151420.19265625X-RAY DIFFRACTION100
6.5-15.130.21551450.18255744X-RAY DIFFRACTION99
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)
13.5611-0.9612-0.55224.5033-0.81992.70860.24150.16630.1725-0.6963-0.1491-0.392-0.88820.0686-0.0590.7135-0.15120.16480.431-0.15840.532230.34998.877454.2643
20.75870.16980.65432.90430.99552.8086-0.21350.20350.1929-0.68020.4974-0.3003-0.62910.3828-0.24420.568-0.11760.10890.67-0.20440.624235.6984.641449.1011
30.0477-0.2250.25382.7134-0.05131.90390.1168-0.1087-0.08780.10440.1174-0.0743-0.13490.1215-0.15980.34020.03350.09730.4449-0.23030.467824.360582.706661.6918
40.89360.9217-1.58413.3853-0.52793.2920.4315-0.22280.21410.4347-0.12460.5489-0.4813-0.1646-0.26170.4907-0.01210.0190.548-0.21360.600515.070485.777171.2153
51.0156-0.6261-0.45992.89681.19352.6736-0.0544-0.10180.27480.72790.16670.05320.06330.2225-0.160.39370.00380.04740.4687-0.12580.46521.44381.282270.8313
63.31671.00022.38796.97671.89522.3585-0.0103-1.0853-0.3271.0235-0.3321-0.02061.4114-0.09550.27380.5950.1072-0.06330.6349-0.11810.639532.121264.88569.6823
73.6485-0.9302-0.81672.0082-0.26452.4063-0.0890.1060.3116-0.26330.0190.1781-0.35440.0870.08940.4099-0.0399-0.01030.38830.01870.332213.519743.1614-13.3706
83.2186-2.47791.4837.1145-0.40713.3154-0.07740.94580.1739-1.349-0.027-0.3079-0.4868-0.15850.09840.604-0.11560.05670.62990.00470.453517.689632.056-22.6139
91.18790.3350.66391.94631.0581.5921-0.0120.0807-0.1445-0.29420.0548-0.1380.00470.1318-0.03740.3045-0.06460.01140.3174-0.0040.292719.526126.1507-7.4551
101.0019-0.0310.93640.68260.57371.39470.00230.10260.1421-0.1186-0.02230.0879-0.11910.05340.06640.30620.01180.01050.3643-0.05050.42697.303634.19770.6611
112.03080.03491.36161.46810.53171.605-0.21270.051-0.18610.2161-0.03340.18140.0536-0.31670.06450.4138-0.08340.05590.4912-0.10090.4196-1.960529.89716.6975
125.9647-3.57891.1883.2464-0.44221.8102-0.7953-0.5892-0.24370.4820.54490.1180.2346-0.3960.1950.4383-0.00330.03060.4696-0.08030.48770.753532.284518.2544
132.4797-0.18960.44082.44240.55363.2199-0.0369-0.02930.162-0.2660.06940.14120.0173-0.11250.09440.38970.0193-0.03960.2779-0.0490.4123-0.243137.53230.0059
142.6564-0.5305-1.73421.52521.29512.5233-0.1131-0.3478-0.19790.25310.1646-0.01360.62120.5127-0.05970.48550.00280.0010.3938-0.00380.375922.102711.89362.4564
152.9787-0.8303-0.1862.1653-0.02841.2704-0.02180.91370.0984-0.7446-0.1421-0.05690.1166-0.83220.07930.935-0.13920.03331.0538-0.1790.630414.43511.3352-40.6186
163.1061-0.4543-1.24132.29890.38031.7987-0.20431.0444-0.0165-0.68110.2955-0.5353-0.15310.0136-0.13251.0164-0.26470.21471.0984-0.25520.594727.25533.4512-44.1792
171.33860.42490.04080.4499-0.19350.9549-0.26930.2161-0.6487-0.6670.2291-0.19640.5931-0.10810.12630.7745-0.20140.19130.7335-0.33140.655424.0229-6.9789-32.2187
182.2772-0.6365-0.89651.0910.75181.8864-0.17860.4537-0.1729-0.2477-0.02760.05120.3816-0.416-0.06280.6386-0.18940.07580.7303-0.15060.480312.97130.6319-28.9521
192.1715-0.7778-2.01743.97750.79731.8722-0.13290.328-0.7515-0.1990.37930.28870.321-0.0306-0.13890.6823-0.1620.04660.6924-0.19710.59632.3896-5.4478-23.6514
204.0719-0.7721-0.8512.45180.06921.6217-0.29320.3325-0.55140.25350.33770.6620.1038-0.1921-0.05550.5698-0.16250.00980.6664-0.10610.58591.00655.1428-17.6395
211.56920.2288-1.41942.46730.48161.7989-0.26280.4566-0.3657-0.11780.1474-0.09710.4971-0.10280.12190.6473-0.15420.06270.5606-0.17310.570512.9186-6.1957-21.8396
224.3048-0.8959-2.42932.84340.55682.9539-0.4788-0.5195-1.09860.20630.2576-0.30720.89721.01340.00170.96280.01030.15620.6447-0.18370.900630.0495-15.9655-23.2494
235.16710.5130.5122.37641.67883.33680.1967-0.1024-0.07580.7462-0.29450.1573-1.16331.22750.24390.8041-0.21270.03770.9044-0.15980.682726.4434100.598982.6826
240.8693-0.05760.80682.0602-0.51071.9817-0.43750.2396-0.5611.2182-0.314-0.40090.1994-0.17980.5470.952-0.19680.08570.8112-0.2740.712232.757683.831382.4455
250.331-0.1536-0.34890.99070.92670.9131-0.2540.0126-0.01930.38810.3587-0.03240.63190.6903-0.24990.66450.05650.070.7367-0.1820.648142.443130.26965.567
263.16280.2158-1.69244.2268-0.74424.9936-0.36450.3211-0.40420.03480.01710.34922.2079-0.4880.27121.1781-0.12270.10370.6627-0.14130.84095.286253.42369.2956
271.5546-0.003-0.75260.5727-0.66151.1240.02020.019-0.40360.16860.1878-0.2011-0.11410.3585-0.32020.72190.07160.11440.5125-0.06610.674411.545464.949480.8134
281.76111.4981.11972.1806-0.35972.59260.2438-0.76580.70630.5195-0.027-0.62680.0550.8739-0.17721.01730.10940.09111.29790.04680.829215.042366.5704101.7219
293.21090.9085-0.13210.9586-0.87911.2190.5887-0.8084-0.44530.8734-0.0692-0.97711.2150.9723-0.65421.28680.3516-0.14651.18120.06771.008221.83156.1213109.5318
301.54060.7665-1.08571.83140.08332.4238-0.035-0.4556-0.44390.3858-0.08380.14611.13570.58610.29621.09590.07920.26890.71290.06840.78782.19555.055797.2392
311.75960.33810.40750.40290.390.37870.4569-0.7818-1.38981.580.3271-0.50840.54250.7342-0.37561.56010.6003-0.11241.47660.06271.82027.922743.7129108.4162
320.58870.82860.55462.0031.25240.7881-0.60930.9177-0.51151.34620.38560.03950.6154-0.5629-0.39031.51240.09850.19680.83040.14391.1923-4.772844.1798100.3319
332.11340.1774-1.55951.158-0.58973.6407-0.41640.0247-0.27230.27960.32790.21150.20520.02060.03550.77850.11060.15210.49190.10580.56560.209662.765193.1648
343.06020.2384-0.4722.4654-0.95545.4069-0.64630.5798-0.36260.030.3180.48330.7357-0.68840.39680.758-0.13280.08160.9265-0.02030.9668-7.29758.099179.3031
354.0598-1.5498-0.20022.7507-0.24763.33640.0006-0.01310.70750.00470.02270.2687-0.9407-0.0488-0.0690.62650.01950.02480.3909-0.00280.570816.439474.774222.0547
361.7741-0.80790.56324.41270.96872.742-0.17270.30430.1438-0.43850.23570.1142-0.47950.1187-0.14790.4929-0.07060.05310.5377-0.0390.399724.813260.749812.937
371.23290.38450.86371.69960.53681.40750.0115-0.0280.0204-0.10710.0665-0.3601-0.13150.0993-0.12480.2525-0.00630.03190.3019-0.11640.319221.054554.36326.4893
380.4424-0.8977-0.98962.49921.58992.5007-0.0424-0.7049-0.5298-0.8222-0.30320.2257-0.2123-0.8441-0.11630.28180.066-0.06340.483-0.04910.54332.667357.669824.7163
391.74421.05160.47090.87440.95751.92290.0561-0.11180.27540.06470.1819-0.125-0.31760.2272-0.15140.372-0.03140.04260.3393-0.1610.407918.879764.493238.5769
401.7566-0.9847-0.09322.44461.90014.5518-0.26010.1749-0.0388-0.1057-0.42090.0544-0.3005-1.32960.56620.66760.10640.03250.7247-0.21570.7094-4.124865.518234.9086
412.5132-1.09340.50682.29090.64362.978-0.1498-0.39580.24130.15620.00110.273-0.3966-0.81960.22020.41550.04340.00290.5432-0.20660.46896.584963.192644.5122
420.8024-0.3739-0.00552.47672.21943.8238-0.1647-0.1941-0.17070.4570.04350.09070.67220.1665-0.05790.35080.03640.02280.4457-0.01440.414920.755541.729132.074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 259 )
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 306 )
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 414 )
6X-RAY DIFFRACTION6chain 'A' and (resid 415 through 439 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 72 )
8X-RAY DIFFRACTION8chain 'C' and (resid 73 through 102 )
9X-RAY DIFFRACTION9chain 'C' and (resid 103 through 223 )
10X-RAY DIFFRACTION10chain 'C' and (resid 224 through 281 )
11X-RAY DIFFRACTION11chain 'C' and (resid 282 through 324 )
12X-RAY DIFFRACTION12chain 'C' and (resid 325 through 350 )
13X-RAY DIFFRACTION13chain 'C' and (resid 351 through 381 )
14X-RAY DIFFRACTION14chain 'C' and (resid 382 through 440 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 56 )
16X-RAY DIFFRACTION16chain 'D' and (resid 57 through 140 )
17X-RAY DIFFRACTION17chain 'D' and (resid 141 through 214 )
18X-RAY DIFFRACTION18chain 'D' and (resid 215 through 268 )
19X-RAY DIFFRACTION19chain 'D' and (resid 269 through 311 )
20X-RAY DIFFRACTION20chain 'D' and (resid 312 through 338 )
21X-RAY DIFFRACTION21chain 'D' and (resid 339 through 401 )
22X-RAY DIFFRACTION22chain 'D' and (resid 402 through 441 )
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 20 )
24X-RAY DIFFRACTION24chain 'E' and (resid 21 through 46 )
25X-RAY DIFFRACTION25chain 'E' and (resid 47 through 140 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 48 )
27X-RAY DIFFRACTION27chain 'F' and (resid 49 through 83 )
28X-RAY DIFFRACTION28chain 'F' and (resid 84 through 127 )
29X-RAY DIFFRACTION29chain 'F' and (resid 128 through 175 )
30X-RAY DIFFRACTION30chain 'F' and (resid 176 through 222 )
31X-RAY DIFFRACTION31chain 'F' and (resid 223 through 242 )
32X-RAY DIFFRACTION32chain 'F' and (resid 243 through 274 )
33X-RAY DIFFRACTION33chain 'F' and (resid 275 through 339 )
34X-RAY DIFFRACTION34chain 'F' and (resid 340 through 380 )
35X-RAY DIFFRACTION35chain 'B' and (resid 1 through 64 )
36X-RAY DIFFRACTION36chain 'B' and (resid 65 through 128 )
37X-RAY DIFFRACTION37chain 'B' and (resid 129 through 214 )
38X-RAY DIFFRACTION38chain 'B' and (resid 215 through 238 )
39X-RAY DIFFRACTION39chain 'B' and (resid 239 through 273 )
40X-RAY DIFFRACTION40chain 'B' and (resid 274 through 295 )
41X-RAY DIFFRACTION41chain 'B' and (resid 296 through 373 )
42X-RAY DIFFRACTION42chain 'B' and (resid 374 through 438 )

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