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- PDB-6elu: Structure of Serum Resistance Associated protein from T. b. rhode... -

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Basic information

Entry
Database: PDB / ID: 6elu
TitleStructure of Serum Resistance Associated protein from T. b. rhodesiense
Components
  • G10_3 Light chain
  • G10_3 heavy chain
  • Serum resistance associated; VSG protein
KeywordsANTITOXIN / Tryanosome / innate immune evasion / sleeping sickness / apolipoprotein LI / SRA / trypanolytic factor.
Function / homology
Function and homology information


: / evasion of host immune response / plasma membrane
Similarity search - Function
Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serum resistance associated; VSG protein
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZoll, S. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P001424/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2018
Title: The structure of serum resistance-associated protein and its implications for human African trypanosomiasis.
Authors: Zoll, S. / Lane-Serff, H. / Mehmood, S. / Schneider, J. / Robinson, C.V. / Carrington, M. / Higgins, M.K.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum resistance associated; VSG protein
B: G10_3 heavy chain
C: G10_3 Light chain
D: Serum resistance associated; VSG protein
E: G10_3 heavy chain
F: G10_3 Light chain
G: Serum resistance associated; VSG protein
H: G10_3 heavy chain
I: G10_3 Light chain
J: Serum resistance associated; VSG protein
K: G10_3 heavy chain
L: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)292,14812
Polymers292,14812
Non-polymers00
Water10,449580
1
A: Serum resistance associated; VSG protein
B: G10_3 heavy chain
C: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Serum resistance associated; VSG protein
E: G10_3 heavy chain
F: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Serum resistance associated; VSG protein
H: G10_3 heavy chain
I: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Serum resistance associated; VSG protein
K: G10_3 heavy chain
L: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.600, 103.550, 150.640
Angle α, β, γ (deg.)90.00, 114.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serum resistance associated; VSG protein


Mass: 24399.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: SRA / Production host: Escherichia coli (E. coli) / Strain (production host): T7 shuffle / References: UniProt: Q8T309
#2: Antibody
G10_3 heavy chain


Mass: 24693.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody
G10_3 Light chain


Mass: 23944.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dehydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM tris(base)/Bicine pH 8.5, ...Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dehydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM tris(base)/Bicine pH 8.5, 20% (v/v) PEG 500 MME, 10 % (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→48.431 Å / Num. obs: 310049 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.431 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.66
RfactorNum. reflection% reflection
Rfree0.2204 7914 5 %
Rwork0.1905 --
obs0.192 158272 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18573 0 0 580 19153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718966
X-RAY DIFFRACTIONf_angle_d1.00225843
X-RAY DIFFRACTIONf_dihedral_angle_d7.60811433
X-RAY DIFFRACTIONf_chiral_restr0.0563005
X-RAY DIFFRACTIONf_plane_restr0.0063307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.36962610.34444974X-RAY DIFFRACTION100
2.3261-2.35350.34042650.32575030X-RAY DIFFRACTION100
2.3535-2.38220.32112610.31584961X-RAY DIFFRACTION100
2.3822-2.41240.34922640.30235018X-RAY DIFFRACTION100
2.4124-2.44410.33082610.29634946X-RAY DIFFRACTION100
2.4441-2.47760.32452620.28354982X-RAY DIFFRACTION100
2.4776-2.5130.28412640.27555023X-RAY DIFFRACTION100
2.513-2.55050.30922630.27114989X-RAY DIFFRACTION100
2.5505-2.59030.29492630.26214995X-RAY DIFFRACTION100
2.5903-2.63280.30852610.25734968X-RAY DIFFRACTION100
2.6328-2.67820.29132620.2544983X-RAY DIFFRACTION100
2.6782-2.72690.28722680.24215073X-RAY DIFFRACTION100
2.7269-2.77930.25482600.22474949X-RAY DIFFRACTION100
2.7793-2.8360.26052630.21755002X-RAY DIFFRACTION100
2.836-2.89770.25612640.2195020X-RAY DIFFRACTION100
2.8977-2.96510.2722630.22014995X-RAY DIFFRACTION100
2.9651-3.03920.27832640.22195014X-RAY DIFFRACTION100
3.0392-3.12140.27462630.22944993X-RAY DIFFRACTION100
3.1214-3.21320.26462630.21734997X-RAY DIFFRACTION100
3.2132-3.31690.25982620.20634983X-RAY DIFFRACTION100
3.3169-3.43540.23672650.20035038X-RAY DIFFRACTION100
3.4354-3.5730.22662660.18845048X-RAY DIFFRACTION100
3.573-3.73550.20892630.1774995X-RAY DIFFRACTION100
3.7355-3.93240.20352630.15985003X-RAY DIFFRACTION100
3.9324-4.17860.16142650.1555038X-RAY DIFFRACTION100
4.1786-4.5010.16182660.13625043X-RAY DIFFRACTION100
4.501-4.95360.17632650.12935043X-RAY DIFFRACTION100
4.9536-5.66940.17032650.14315029X-RAY DIFFRACTION100
5.6694-7.13920.16862670.16735076X-RAY DIFFRACTION100
7.1392-48.44180.17412720.16645150X-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)
10.02830.00330.03560.00760.036-0.01210.18740.01170.08480.11640.10640.0161-0.12240.049100.4485-0.1083-0.04030.9371-0.32131.0115133.741333.3475122.6668
2-0.0040.00440.0120.0022-0.0009-0.00670.1080.02340.05040.00650.04040.0035-0.0328-0.027500.8806-0.05910.00110.9326-0.17990.9479125.486840.274116.2138
30.01150.01110.00670.00720.00480.00150.0805-0.00980.03380.01550.0364-0.0292-0.01920.056300.5417-0.0654-0.07060.8073-0.16570.7739134.310311.8073105.5124
40.01130.03830.04070.0355-0.03240.0248-0.0849-0.14510.06530.11630.1683-0.14340.3670.123900.43370.054-0.05660.2415-0.03450.3635115.0412-7.691101.8223
5-0.04440.0259-0.02270.0521-0.0008-0.00230.25950.2132-0.10450.1227-0.0047-0.09710.07250.0462-00.5672-0.14740.0263-1.2782-0.06570.27597.8784-20.659776.5779
6-0.0095-0.00770.00390.0264-0.00320.00360.0395-0.11330.0817-0.0972-0.0677-0.0184-0.02710.0325-00.5645-0.03190.06260.2863-0.06410.4746110.299115.394992.2454
70.0094-0.00480.01310.0068-0.01520.01110.1244-0.03420.0616-0.19220.0455-0.0151-0.06440.1351-00.4701-0.14970.10120.1364-0.13670.3849114.92618.876986.5998
80.0188-0.06930.00650.03580.00910.02140.014-0.24540.00060.02180.1054-0.02870.0102-0.007100.425-0.22250.0604-0.4273-0.02190.279998.7826-4.479582.6496
9-0.0007-0.0257-0.00470.031-0.0211-0.01180.03530.02970.05590.1335-0.00760.0332-0.0498-0.4585-00.3627-0.25190.2145-1.02710.41740.154985.3223-10.03273.4512
100.0122-0.00260.0133-0.00340.00740.00020.0992-0.02480.13990.0032-0.0020.05780.0520.0374-00.9013-0.1365-0.38751.0321-0.09260.907175.94256.619360.9951
110.0037-00.0106-00.00390.00550.0466-0.02270.07230.0031-0.02910.06870.11310.036400.887-0.1772-0.26481.0579-0.18160.9258170.873811.434872.0715
120.00040.00040-0.0019-0.0002-0.0002-0.0056-0.00270.0003-0.0078-0.0010.02110.0135-0.012401.43870.05380.00191.4059-0.01181.3888174.3926-10.900263.7689
130.00530.00160.0037-0.00210.00390.0004-0.02640.0048-0.0224-0.0147-0.03770.00360.04030.0002-00.7715-0.1755-0.24080.9005-0.10780.883161.11489.999168.2979
140.00020.00020.00020.00010.00020.0031-0.0029-0.00390.0036-0.0021-0.00130.0041-0.0011-0.003-01.20610.02250.01751.2404-0.05611.1964143.547321.04979.9459
150.00130.00060.004-0.001-0.00010.00050.02410.0137-0.00050.02810.0146-0.05660.00970.0186-00.706-0.1475-0.18070.8108-0.08440.8309153.422417.609164.205
160.03350.0265-0.00220.0394-0.06150.03620.13330.04110.2384-0.0576-0.0849-0.2403-0.0351-0.0152-00.3573-0.0330.02010.2816-0.05060.3695133.267417.67249.518
17-0.00230.00720.00040.0010.00550.0025-0.0065-0.0085-0.0431-0.0045-0.01430.0662-0.0133-0.0265-00.37140.0009-0.00540.15290.04930.381192.29662.992547.1065
180.0278-0.0070.02010.0303-0.01040.0096-0.01690.09890.01650.01760.03670.1105-0.09790.054100.36710.07710.03450.16190.04070.2294103.04989.823447.4272
190.0035-0.00280.00830.0025-0.00320.0053-0.0707-0.0032-0.03680.1062-0.0823-0.03310.10230.0306-00.40110.0605-0.06050.4590.00770.4621138.1132-5.218559.7912
200.00180.005200.0098-0.00320.00640.0213-0.0540.01390.0822-0.04030.0058-0.02870.097-00.31760.0081-0.090.38410.00360.2915133.22641.459364.6994
210.0013-0.00870.00110.02960.0040.00460.02670.01370.00640.14550.0592-0.03660.16780.1455-00.25810.0398-0.0490.2386-0.03570.2449127.6227-2.496959.2305
220.0046-0.0257-0.00360.04710.02230.0344-0.11450.29570.0160.0829-0.04530.0257-0.0343-0.1265-00.32380.18680.0060.155-0.08760.2115100.6817-5.874942.8945
230.008-0.00170.0129-0.0003-0.00180.01160.1759-0.01280.04050.1336-0.06420.02140.01970.043100.73050.1256-0.18011.10.07860.8163135.8328-41.178363.7673
240.00050.00130.0004-0.00060.001-0.0003-0.0058-0.0075-0.00780.017-0.0033-0.00580.00160.0027-01.3439-0.04980.08361.41630.00851.4277125.5524-27.974376.2601
250.00840.00050.0101-0.0055-0.00010.00410.018-0.02670.0215-0.014-0.0041-0.10120.0072-0.00700.56050.0963-0.11960.76270.01520.5655135.4012-37.1347.0464
26-0.00080.00210.00550.00250.00360.0058-0.03210.0222-0.011-0.0297-0.0116-0.04210.01780.0123-00.55930.1736-0.14040.5984-0.01070.5343131.0466-44.178441.578
270.02150.00830.01910.0626-0.01260.0259-0.21390.09290.0294-0.0240.1973-0.03620.30960.10700.31850.18240.03830.3211-0.07890.2775112.496-46.831925.2559
28-0.0017-0.0032-0.0020.0003-0.00020.0028-0.04430.01750.02820.0101-0.03420.01080.016-0.0098-00.2909-0.005-0.01750.46260.0260.252689.6595-25.2674-4.8324
290.02160.00180.03020.01180.00890.01220.06760.30560.01960.1111-0.06620.04420.13230.0453-00.228-0.01550.00470.3958-0.02190.179396.6402-33.571.7324
300.0008-0.0094-0.01680.00030.00290.0046-0.0082-0.04860.0756-0.05150.039-0.0044-0.00110.0198-00.32210.03450.01680.2733-0.04620.2956107.2951-21.686334.5346
310.0059-0.01270.00440.02050.020.00240.02620.02770.1467-0.0023-0.0354-0.1703-0.06690.067700.27860.0628-0.09840.2794-0.10230.3011117.3703-27.081233.5855
320.0166-0.0059-0.0010.01320.02420.0145-0.01980.05650.07910.04380.0156-0.04840.03660.03900.31360.0617-0.02260.2831-0.02950.2883111.9183-28.410631.2504
330.0081-0.03230.01310.00380.0132-0.00540.04890.2049-0.01530.13330.05860.0137-0.1605-0.1312-00.11660.013-0.00250.3253-0.02440.240192.2585-23.60468.1179
340.0053-0.003-0.00530.0124-0.00590.0064-0.08690.04280.00220.1158-0.03640.0384-0.01-0.0153-00.2341-0.01560.02330.3921-0.010.303384.8551-20.98399.7568
350.0003-0.00130.00040.0027-0.0020.0025-0.0381-0.0009-0.00090.0388-0.0166-0.05560.0159-0.049100.247-0.01230.0090.3359-0.00190.25294.756-23.071714.2181
360.0055-0.00940.00620.0030.00410.00180.01160.0558-0.04460.00150.01430.1074-0.0636-0.1023-00.18180.0254-0.02520.4137-0.00470.325279.9067-22.21873.7265
370.0740.00050.05240.12850.0486-0.0024-0.22680.2674-0.0469-1.1820.0402-0.5020.00660.0634-0-0.80130.6252-0.37980.61230.31220.2687173.9531-17.397513.0316
380.0010.00180.00080.00050.0116-0.00380.0065-0.0099-0.0054-0.0785-0.03860.00340.07270.018-00.78830.01860.13680.9063-0.01740.8033172.4758-23.7205-2.0985
390.0058-0.00690.00430.0008-0.00490.0048-0.07680.0667-0.09110.1791-0.1504-0.0441-0.04980.071600.26540.1301-0.08020.5749-0.04080.499155.7661-11.134122.9548
400.03480.00850.00380.06910.01440.00240.03470.1351-0.02410.10250.05630.2205-0.07070.234700.2497-0.00140.0370.51320.07270.2505136.90116.978613.7841
410.0034-0.00490.00310.0031-0.0038-0.0028-0.01240.03950.0391-0.0204-0.0412-0.02810.0107-0.003700.3782-0.0550.04720.57940.20810.729895.29675.79911.2991
420.014-0.01080.01120.01620.01060.00730.05790.01690.0810.07740.02870.0735-0.06090.035600.25780.04050.07130.36370.15670.4804106.54258.14726.6985
430.0034-0.0032-0.00270.00120.00190.00320.04780.0039-0.0333-0.05430.05540.0416-0.02320.046400.2959-0.02950.0540.5443-0.04120.4099131.5475-15.1316-1.5838
440.00770.00630.00080.00370.0060.0069-0.00030.1096-0.0122-0.02750.11830.0319-0.05280.0697-00.17990.05470.02030.4646-0.0940.2891138.2433-11.89067.0593
450.03710.090.00110.0631-0.00120.0635-0.12090.2379-0.0179-0.09360.2126-0.02170.0020.112200.21640.00390.00110.4228-0.02550.3416125.6606-9.79224.3585
46-0.0226-0.018-0.01030.01930.0339-0.0002-0.10890.1920.181-0.13370.15390.00570.18390.03730-0.20160.127-0.48580.52530.46550.0109103.55151.2112-9.3137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 254 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 127 )
5X-RAY DIFFRACTION5chain 'B' and (resid 128 through 222 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 36 )
7X-RAY DIFFRACTION7chain 'C' and (resid 37 through 94 )
8X-RAY DIFFRACTION8chain 'C' and (resid 95 through 132 )
9X-RAY DIFFRACTION9chain 'C' and (resid 133 through 217 )
10X-RAY DIFFRACTION10chain 'D' and (resid 46 through 80 )
11X-RAY DIFFRACTION11chain 'D' and (resid 81 through 115 )
12X-RAY DIFFRACTION12chain 'D' and (resid 116 through 175 )
13X-RAY DIFFRACTION13chain 'D' and (resid 176 through 205 )
14X-RAY DIFFRACTION14chain 'D' and (resid 206 through 213 )
15X-RAY DIFFRACTION15chain 'D' and (resid 214 through 252 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 127 )
17X-RAY DIFFRACTION17chain 'E' and (resid 128 through 142 )
18X-RAY DIFFRACTION18chain 'E' and (resid 143 through 222 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 36 )
20X-RAY DIFFRACTION20chain 'F' and (resid 37 through 79 )
21X-RAY DIFFRACTION21chain 'F' and (resid 80 through 117 )
22X-RAY DIFFRACTION22chain 'F' and (resid 118 through 217 )
23X-RAY DIFFRACTION23chain 'G' and (resid 46 through 120 )
24X-RAY DIFFRACTION24chain 'G' and (resid 121 through 174 )
25X-RAY DIFFRACTION25chain 'G' and (resid 175 through 213 )
26X-RAY DIFFRACTION26chain 'G' and (resid 214 through 252 )
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 127 )
28X-RAY DIFFRACTION28chain 'H' and (resid 128 through 142 )
29X-RAY DIFFRACTION29chain 'H' and (resid 143 through 222 )
30X-RAY DIFFRACTION30chain 'I' and (resid 1 through 25 )
31X-RAY DIFFRACTION31chain 'I' and (resid 26 through 79 )
32X-RAY DIFFRACTION32chain 'I' and (resid 80 through 105 )
33X-RAY DIFFRACTION33chain 'I' and (resid 106 through 132 )
34X-RAY DIFFRACTION34chain 'I' and (resid 133 through 159 )
35X-RAY DIFFRACTION35chain 'I' and (resid 160 through 178 )
36X-RAY DIFFRACTION36chain 'I' and (resid 179 through 217 )
37X-RAY DIFFRACTION37chain 'J' and (resid 45 through 119 )
38X-RAY DIFFRACTION38chain 'J' and (resid 120 through 183 )
39X-RAY DIFFRACTION39chain 'J' and (resid 184 through 252 )
40X-RAY DIFFRACTION40chain 'K' and (resid 1 through 127 )
41X-RAY DIFFRACTION41chain 'K' and (resid 128 through 142 )
42X-RAY DIFFRACTION42chain 'K' and (resid 143 through 222 )
43X-RAY DIFFRACTION43chain 'L' and (resid 1 through 18 )
44X-RAY DIFFRACTION44chain 'L' and (resid 19 through 52 )
45X-RAY DIFFRACTION45chain 'L' and (resid 53 through 132 )
46X-RAY DIFFRACTION46chain 'L' and (resid 133 through 217 )

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