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- PDB-5i4a: X-ray crystal structure of Marinitoga piezophila Argonaute in com... -

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Basic information

Entry
Database: PDB / ID: 5i4a
TitleX-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA
Components
  • Argonaute protein
  • RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / Argonaute / 5' OH / Guide RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / DNA endonuclease activity / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Piwi domain / Piwi / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesMarinitoga piezophila (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.949 Å
AuthorsDoxzen, K.W. / Kaya, E. / Knoll, K.R. / Wilson, R.C. / Strutt, S.C. / Kranzusch, P.J. / Doudna, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: A bacterial Argonaute with noncanonical guide RNA specificity.
Authors: Kaya, E. / Doxzen, K.W. / Knoll, K.R. / Wilson, R.C. / Strutt, S.C. / Kranzusch, P.J. / Doudna, J.A.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Jul 6, 2016Group: Data collection
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Argonaute protein
B: RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')
C: Argonaute protein
D: RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)165,4584
Polymers165,4584
Non-polymers00
Water12,683704
1
A: Argonaute protein
B: RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)82,7292
Polymers82,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Argonaute protein
D: RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)82,7292
Polymers82,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.883, 75.420, 102.215
Angle α, β, γ (deg.)110.87, 90.55, 90.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Argonaute protein / MpAgo


Mass: 76190.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinitoga piezophila (strain DSM 14283 / JCM 11233 / KA3) (bacteria)
Strain: DSM 14283 / JCM 11233 / KA3 / Gene: Marpi_0405 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2J4R4
#2: RNA chain RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')


Mass: 6538.916 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 27% PEG 2,000, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587,0.97964,0.97197
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
20.979641
30.971971
ReflectionResolution: 1.949→48.33 Å / Num. obs: 100295 / % possible obs: 96.7 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6
Reflection shellResolution: 1.949→1.98 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 1.2 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.949→48.327 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 4003 2.01 %
Rwork0.2157 --
obs0.2161 198823 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→48.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10664 437 0 704 11805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311399
X-RAY DIFFRACTIONf_angle_d0.57815459
X-RAY DIFFRACTIONf_dihedral_angle_d14.9366863
X-RAY DIFFRACTIONf_chiral_restr0.0451702
X-RAY DIFFRACTIONf_plane_restr0.0031870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9487-1.97160.31121140.3534955X-RAY DIFFRACTION71
1.9716-1.99560.3691300.34136534X-RAY DIFFRACTION95
1.9956-2.02090.3391320.33366806X-RAY DIFFRACTION95
2.0209-2.04750.33381410.3156671X-RAY DIFFRACTION95
2.0475-2.07550.32941380.31166599X-RAY DIFFRACTION95
2.0755-2.10520.28281360.30176801X-RAY DIFFRACTION96
2.1052-2.13660.30871300.29536606X-RAY DIFFRACTION95
2.1366-2.170.28091540.28366733X-RAY DIFFRACTION96
2.17-2.20560.30481430.27946759X-RAY DIFFRACTION96
2.2056-2.24360.31081270.27266651X-RAY DIFFRACTION96
2.2436-2.28440.27011520.26636775X-RAY DIFFRACTION96
2.2844-2.32830.27871480.25696756X-RAY DIFFRACTION96
2.3283-2.37590.28191340.25686645X-RAY DIFFRACTION96
2.3759-2.42750.28091400.25766796X-RAY DIFFRACTION96
2.4275-2.4840.2971380.25726715X-RAY DIFFRACTION96
2.484-2.54610.31131330.25126847X-RAY DIFFRACTION97
2.5461-2.61490.2481390.23556703X-RAY DIFFRACTION97
2.6149-2.69190.23881330.23036887X-RAY DIFFRACTION97
2.6919-2.77880.24521290.24036716X-RAY DIFFRACTION97
2.7788-2.87810.25631380.22866791X-RAY DIFFRACTION97
2.8781-2.99330.23231460.22726865X-RAY DIFFRACTION97
2.9933-3.12950.27841390.20816764X-RAY DIFFRACTION97
3.1295-3.29440.24781390.20436813X-RAY DIFFRACTION98
3.2944-3.50080.21181460.19636886X-RAY DIFFRACTION98
3.5008-3.7710.20791420.17966899X-RAY DIFFRACTION99
3.771-4.15030.19221360.17266969X-RAY DIFFRACTION99
4.1503-4.75040.19551340.16166954X-RAY DIFFRACTION99
4.7504-5.98320.2011400.17126973X-RAY DIFFRACTION99
5.9832-48.34150.18421520.18426951X-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)
10.1059-0.021-0.01590.00490.00690.0011-0.06-0.06470.0607-0.13260.009-0.07920.13340.0034-0.02920.4449-0.1481-0.02280.2012-0.020.270525.671347.510656.4278
20.0216-0.0059-0.00470.01920.01420.0134-0.096-0.11470.00760.17480.00240.06340.04460.0138-0.00180.3274-0.09380.03910.2964-0.07930.368530.201660.26178.6983
30.05010.0302-0.04040.06120.00430.0365-0.04010.0722-0.0303-0.12760.1075-0.28240.04990.33410.00010.4311-0.0422-0.00330.3641-0.03270.429332.948657.216166.7338
40.00870.00980.00930.01210.00180.0150.0421-0.006-0.0091-0.0150.023-0.00540.0550.01030.010.3656-0.1660.00480.1134-0.05010.282623.590247.641264.0084
50.00510.0023-0.00150.00290.0020.00580.0672-0.0347-0.0426-0.00180.0991-0.00210.02410.01980.00020.3787-0.12160.04380.2628-0.03540.467313.098644.470770.3253
60.00560.00020.00030.00350.00350.00180.0056-0.0338-0.041-0.02480.00460.0806-0.0095-0.0811-00.5665-0.11970.00110.6918-0.05780.8041-3.778444.346171.5417
70.0543-0.0074-0.03920.2609-0.10740.1624-0.0411-0.02190.0397-0.2705-0.01980.20620.0966-0.0181-0.05670.5248-0.2357-0.03430.1967-0.0580.339313.310939.782162.035
80.00950.01160.00820.01140.01020.0209-0.1414-0.04510.03560.0951-0.10110.18270.02740.0977-0.00020.71740.02740.08840.789-0.01210.45537.189241.403786.1627
90.0374-0.0134-0.00790.0148-0.00660.0377-0.1285-0.1468-0.10420.15710.0048-0.0390.09060.138500.8147-0.06670.03050.7047-0.0320.71835.935138.103983.559
100.0030.00150.00080.0029-00.0032-0.02710.01920.0043-0.02720.0080.0197-0.00720.0083-00.7302-0.2857-0.05220.8605-0.05750.7123-4.426632.997565.598
110.0179-0.02540.00380.0228-0.00580.0150.03250.17290.1295-0.106-0.11060.1974-0.0022-0.2397-0.00010.8118-0.0866-0.07150.52620.03010.44429.737145.208853.7508
120.03410.0526-0.01370.1933-0.1110.0780.01320.05590.0856-0.6380.06230.1670.05680.02670.1290.5246-0.1674-0.07510.153-0.04330.05719.19722.257260.1959
130.0220.0074-0.00320.00580.00980.03790.0191-0.06710.0654-0.0370.0790.13340.0245-0.00380.05010.147-0.06590.01660.36040.02980.3145-5.9304-2.937185.056
140.34980.0258-0.07730.1531-0.12620.4371-0.0341-0.3023-0.0411-0.06510.06610.11680.28020.0148-0.15620.0462-0.0768-0.02430.17230.03360.18266.9285-2.502282.6683
150.0051-0.00680.01070.0629-0.01980.02420.00740.0383-0.021-0.10290.07210.04140.025-0.04760.09440.1048-0.0666-0.02470.14070.01980.14584.30312.065370.045
160.2371-0.13780.08860.1267-0.07660.0396-0.0739-0.0050.1603-0.2222-0.2108-0.2447-0.07510.3931-0.04650.3412-0.04810.04650.27760.03470.185622.92757.208361.991
170.0713-0.13160.17260.254-0.35680.49070.0275-0.33730.16830.1411-0.2281-0.1535-0.25160.2503-0.0050.2085-0.09140.02620.62220.07170.341328.147712.828472.1393
180.00370.0009-0.00010.0029-0.00050.0028-0.0385-0.00860.01890.0166-0.02-0.0255-0.0116-0.0141-00.5591-0.326-0.09330.84560.01540.597134.521823.120682.1141
190.1748-0.08160.06460.0414-0.03060.0269-0.0407-0.10210.12860.0112-0.1432-0.1628-0.01360.2052-0.10180.18180.04770.18630.92140.25250.523137.274110.698669.7613
200.04140.01160.01970.0018-0.00010.0237-0.0004-0.08540.06270.0854-0.0806-0.2737-0.05310.365100.5279-0.10280.11640.8640.19120.693435.95917.59462.6098
210.02890.00370.04450.0049-0.01090.1301-0.11450.0097-0.146-0.0452-0.1158-0.27430.06420.20470.00940.4404-0.23230.09070.49720.03540.304133.333518.121258.4752
220.0599-0.06760.00980.077-0.01350.00270.06730.0182-0.0545-0.13750.02470.10990.02970.01370.03010.7294-0.2083-0.02750.2567-0.00410.264913.409627.55553.8392
230.0451-0.08480.09720.1529-0.1790.2097-0.05130.07860.053-0.0978-0.0733-0.1033-0.00770.10940.00590.6292-0.21380.05520.14450.06470.110321.256924.976752.6229
240.00910.0020.02130.07870.02890.0547-0.0389-0.0179-0.0119-0.0987-0.06410.1258-0.0980.016-0.00510.5985-0.20590.06170.4172-0.00360.330917.332123.212158.6423
250.01470.00110.0060.0002-0.00030.00320.0209-0.0078-0.02980.01690.0243-0.02520.01990.02580.00020.43760.02230.19090.5190.04310.444933.490814.039649.4202
260.0645-0.07010.03320.1012-0.05060.01820.05090.12910.0558-0.2976-0.02610.014-0.10780.11780.00630.2058-0.05650.02850.14920.02530.108916.572713.149358.2284
270.03380.04640.03720.06630.06120.0609-0.022-0.02660.02860.0133-0.0393-0.0074-0.02680.0214-0.08530.0303-0.278-0.02270.2856-0.0510.09820.634114.725270.7906
280.00740.0129-0.01350.0424-0.01940.03020.0119-0.05180.03320.025-0.018-0.031-0.02610.06930.0424-0.0176-0.20780.02450.27310.05380.07918.48399.338478.387
290.3368-0.10980.26740.0552-0.1510.46790.1375-0.10040.66380.1189-0.0422-0.0599-0.69230.0374-0.11740.3944-0.1730.25470.3123-0.02670.524412.27827.265474.6971
300.0032-0.0023-0.00410.00160.00210.0067-0.0193-0.02130.00420.0226-0.02140.0332-0.0016-0.02570.00020.51250.12150.05930.2095-0.02760.297439.1124-14.924741.3281
310.0086-0.00490.00040.00380.00110.00150.0017-0.0277-0.01110.0084-0.0077-0.0053-0.0060.008800.51350.1726-0.04270.32870.06450.368648.0112-24.797640.9319
320.02140.01540.00050.0193-0.01750.0328-0.0824-0.0366-0.04060.1146-0.0176-0.0444-0.0756-0.0503-0.03440.18810.08470.04240.335-0.02250.335661.7936-34.960228.83
330.0007-0.00070.00130.007-0.00210.00410.02590.0319-0.0091-0.03510.0203-0.0133-0.0167-0.009700.3133-0.00270.05810.383-0.0750.366761.7791-43.912110.7853
340.0027-0.0026-0.00080.0004-0.00010.0008-0.05640.0649-0.0062-0.1104-0.02540.0896-0.0172-0.01950.00010.26780.0537-0.04120.2589-0.05470.342453.9985-37.340514.616
350.0001-0.0005-0.00260.00170.00190.0064-0.04670.08710.0336-0.0592-0.0179-0.0728-0.04550.115700.29840.08530.00490.14960.00260.412455.4303-32.395819.5625
360.0309-0.01820.01780.03130.0180.0309-0.0267-0.11530.09720.26220.0586-0.1932-0.1460.098700.35270.06060.01420.3133-0.02740.349660.0768-37.357127.4826
370.014-0.0158-0.00760.01330.00530.00530.02680.0221-0.02090.01010.0115-0.0015-0.03730.00350.03590.25150.2082-0.03180.0683-0.1170.257450.9599-26.625328.3864
380.0086-0.00950.00160.008-0.00010.0114-0.00380.026-0.0010.01850.05630.0246-0.00940.013100.40880.0363-0.03490.2038-0.02540.469839.5795-24.53422.4174
390.00750.0010.00180.00060.0022-0.0007-0.02030.06720.0674-0.0260.02680.1726-0.0192-0.1499-00.50460.0261-0.00390.6034-0.02140.583622.9135-23.950320.798
400.0097-0.0114-0.00780.05920.00950.0121-0.0447-0.0445-0.03120.1527-0.0310.0757-0.0962-0.0022-0.030.46790.2834-0.030.0798-0.0770.309139.9076-19.168130.2666
410.0145-0.0121-0.01070.01450.0130.0238-0.10240.0337-0.0192-0.1259-0.1290.0949-0.04410.0857-0.00020.6071-0.0263-0.12210.8086-0.06510.465533.8331-20.73726.1098
420.17850.05140.05030.21750.09390.34150.01310.0424-0.12120.29640.10450.31650.270.02530.21480.41710.09260.0440.2326-0.01990.257134.1038-3.919927.933
430.6183-0.10490.14550.3741-0.0660.2183-0.00380.31030.03870.11760.08530.1914-0.20030.0546-0.22490.060.08680.03640.1650.00580.175233.484922.361613.9846
440.6097-0.20670.05110.64820.05140.6129-0.08940.2838-0.39280.3764-0.1471-0.30710.51350.659-0.9210.17070.2633-0.13230.34980.03940.114854.68392.52129.2864
450.0540.0645-0.00750.2563-0.08210.02630.08320.13370.07880.0444-0.00510.18630.03330.03680.0261-0.50760.50080.1457-0.173-0.10740.060243.0599.075221.3194
46-0.00270.0152-0.01690.0332-0.04890.05520.12680.0153-0.57420.04910.1079-0.05940.53750.0837-0.00160.41130.0826-0.09330.21580.01790.378136.7824-1.582219.6934
470.0037-0.00440.00640.043-0.02130.0160.00510.01020.00930.00040.00410.0031-0.00040.00880.00010.76640.0890.05740.7783-0.01720.646844.8426-27.27886.5123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 123 )
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 153 )
8X-RAY DIFFRACTION8chain 'A' and (resid 154 through 190 )
9X-RAY DIFFRACTION9chain 'A' and (resid 193 through 218 )
10X-RAY DIFFRACTION10chain 'A' and (resid 219 through 228 )
11X-RAY DIFFRACTION11chain 'A' and (resid 229 through 255 )
12X-RAY DIFFRACTION12chain 'A' and (resid 258 through 301 )
13X-RAY DIFFRACTION13chain 'A' and (resid 302 through 316 )
14X-RAY DIFFRACTION14chain 'A' and (resid 317 through 408 )
15X-RAY DIFFRACTION15chain 'A' and (resid 409 through 421 )
16X-RAY DIFFRACTION16chain 'A' and (resid 422 through 450 )
17X-RAY DIFFRACTION17chain 'A' and (resid 453 through 475 )
18X-RAY DIFFRACTION18chain 'A' and (resid 476 through 481 )
19X-RAY DIFFRACTION19chain 'A' and (resid 482 through 504 )
20X-RAY DIFFRACTION20chain 'A' and (resid 505 through 531 )
21X-RAY DIFFRACTION21chain 'A' and (resid 534 through 543 )
22X-RAY DIFFRACTION22chain 'A' and (resid 544 through 562 )
23X-RAY DIFFRACTION23chain 'A' and (resid 563 through 569 )
24X-RAY DIFFRACTION24chain 'A' and (resid 570 through 586 )
25X-RAY DIFFRACTION25chain 'A' and (resid 587 through 591 )
26X-RAY DIFFRACTION26chain 'A' and (resid 592 through 617 )
27X-RAY DIFFRACTION27chain 'A' and (resid 618 through 628 )
28X-RAY DIFFRACTION28chain 'A' and (resid 629 through 639 )
29X-RAY DIFFRACTION29chain 'B' and (resid 1 through 21 )
30X-RAY DIFFRACTION30chain 'C' and (resid 1 through 5 )
31X-RAY DIFFRACTION31chain 'C' and (resid 6 through 10 )
32X-RAY DIFFRACTION32chain 'C' and (resid 11 through 20 )
33X-RAY DIFFRACTION33chain 'C' and (resid 21 through 25 )
34X-RAY DIFFRACTION34chain 'C' and (resid 26 through 37 )
35X-RAY DIFFRACTION35chain 'C' and (resid 38 through 43 )
36X-RAY DIFFRACTION36chain 'C' and (resid 46 through 80 )
37X-RAY DIFFRACTION37chain 'C' and (resid 81 through 98 )
38X-RAY DIFFRACTION38chain 'C' and (resid 99 through 110 )
39X-RAY DIFFRACTION39chain 'C' and (resid 111 through 123 )
40X-RAY DIFFRACTION40chain 'C' and (resid 124 through 153 )
41X-RAY DIFFRACTION41chain 'C' and (resid 154 through 190 )
42X-RAY DIFFRACTION42chain 'C' and (resid 193 through 301 )
43X-RAY DIFFRACTION43chain 'C' and (resid 302 through 439 )
44X-RAY DIFFRACTION44chain 'C' and (resid 440 through 604 )
45X-RAY DIFFRACTION45chain 'C' and (resid 605 through 639 )
46X-RAY DIFFRACTION46chain 'D' and (resid 1 through 11 )
47X-RAY DIFFRACTION47chain 'D' and (resid 20 through 21 )

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