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- PDB-5zqv: Crystal Structure of Protein Phosphate 1 complexed with PP1 bindi... -

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Basic information

Entry
Database: PDB / ID: 5zqv
TitleCrystal Structure of Protein Phosphate 1 complexed with PP1 binding domain of GM
Components
  • Protein phosphatase 1 regulatory subunit 3A
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / Glycogen metabolism / Protein Phosphate 1 holoenzyme
Function / homology
Function and homology information


glycogen binding / regulation of glycogen catabolic process / regulation of glycogen biosynthetic process / PTW/PP1 phosphatase complex / DARPP-32 events / protein phosphatase type 1 complex / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand ...glycogen binding / regulation of glycogen catabolic process / regulation of glycogen biosynthetic process / PTW/PP1 phosphatase complex / DARPP-32 events / protein phosphatase type 1 complex / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / glycogen metabolic process / myosin phosphatase activity / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / transition metal ion binding / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / adherens junction / lung development / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / regulation of translation / presynapse / dendritic spine / perikaryon / chromosome, telomeric region / iron ion binding / cell division / nucleolus / glutamatergic synapse / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. ...: / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Protein phosphatase 1 regulatory subunit 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYu, J. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2011CB910500 China
CitationJournal: FEBS J. / Year: 2018
Title: Structural basis for protein phosphatase 1 recruitment by glycogen-targeting subunits.
Authors: Yu, J. / Deng, T. / Xiang, S.
History
DepositionApr 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Protein phosphatase 1 regulatory subunit 3A
F: Protein phosphatase 1 regulatory subunit 3A
G: Protein phosphatase 1 regulatory subunit 3A
H: Protein phosphatase 1 regulatory subunit 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,27815
Polymers197,4918
Non-polymers7877
Water00
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Protein phosphatase 1 regulatory subunit 3A
H: Protein phosphatase 1 regulatory subunit 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2338
Polymers98,7454
Non-polymers4884
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-35 kcal/mol
Surface area26040 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
F: Protein phosphatase 1 regulatory subunit 3A
G: Protein phosphatase 1 regulatory subunit 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0447
Polymers98,7454
Non-polymers2993
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-37 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.973, 111.973, 195.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 38414.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp1ca, Ppp1a / Production host: Escherichia coli (E. coli)
References: UniProt: P62137, protein-serine/threonine phosphatase
#2: Protein
Protein phosphatase 1 regulatory subunit 3A / Protein phosphatase 1 glycogen-associated regulatory subunit / Protein phosphatase type-1 glycogen ...Protein phosphatase 1 glycogen-associated regulatory subunit / Protein phosphatase type-1 glycogen targeting subunit / RG1


Mass: 10957.751 Da / Num. of mol.: 4 / Mutation: C82S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R3A, PP1G / Production host: Escherichia coli (E. coli) / References: UniProt: Q16821
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION

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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: 60.31 % / Description: rod shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M lithium citrate, 11% poly(ethylene glycol) 3350, 4.5% benzamidine hydrochloride hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 50718 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 89.75 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.096 / Χ2: 1.62 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Χ2% possible all
2.95-37.41.33625330.6081.255100
3-3.067.41.19325480.6741.274100
3.06-3.117.50.93625320.7891.303100
3.11-3.187.40.89625350.8361.28100
3.18-3.257.50.65325430.8991.293100
3.25-3.327.50.69525630.8921.31100
3.32-3.417.50.56925240.9171.335100
3.41-3.57.50.40825430.9621.5199.9
3.5-3.67.50.26225280.9821.402100
3.6-3.727.50.27625520.9811.539100
3.72-3.857.50.22625240.9861.46100
3.85-47.40.1925530.991.66999.9
4-4.197.40.14125660.9941.62799.8
4.19-4.417.40.12325190.9941.79199.8
4.41-4.687.30.10825650.9941.90799.5
4.68-5.047.30.09525160.9971.91499.7
5.04-5.557.30.0925470.9961.8499.9
5.55-6.357.40.08225680.9981.91899.9
6.35-87.50.0825480.9962.19899.6
8-506.90.07524110.9952.75292.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MP0

4mp0


Resolution: 2.95→33.288 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 39.49
RfactorNum. reflection% reflection
Rfree0.2967 2177 5.08 %
Rwork0.2515 --
obs0.2537 42817 84.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 238.95 Å2 / Biso mean: 118.254 Å2 / Biso min: 55.54 Å2
Refinement stepCycle: final / Resolution: 2.95→33.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10136 0 43 0 10179
Biso mean--106.77 --
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210400
X-RAY DIFFRACTIONf_angle_d0.56714038
X-RAY DIFFRACTIONf_chiral_restr0.0391500
X-RAY DIFFRACTIONf_plane_restr0.0031835
X-RAY DIFFRACTIONf_dihedral_angle_d12.1513872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.01410.4316830.39391520160352
3.0141-3.08420.4433730.39541645171855
3.0842-3.16130.3882960.39421732182858
3.1613-3.24670.4385970.40091942203965
3.2467-3.34210.43621270.39232307243477
3.3421-3.44990.41331410.38742617275888
3.4499-3.57310.40281520.35682860301296
3.5731-3.7160.38691600.34852892305298
3.716-3.88480.3541650.33192950311598
3.8848-4.08930.36831720.27862929310198
4.0893-4.3450.25181630.24452922308598
4.345-4.67960.24131600.21912942310298
4.6796-5.1490.25281550.20442915307098
5.149-5.89050.27791660.21662941310798
5.8905-7.40790.26981320.20922955308797
7.4079-33.29010.21511350.17352571270685
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)
18.9693-0.1895-0.10350.6292-0.48550.38730.1878-0.82910.5720.37620.4961-1.1451-0.60431.0906-0.5540.9238-0.2148-0.06351.1285-0.0261.004421.315114.372718.9467
21.91290.4802-0.24081.993-1.33458.0618-0.13880.0070.31210.10760.06620.1031-0.202-0.13320.02580.5297-0.0337-0.04230.75470.0130.79478.372414.89850.6131
31.63511.7786-1.25931.9231-1.26868.8082-0.6532-0.28330.5979-0.36550.2077-0.6464-0.16620.72980.07230.7468-0.201-0.00561.10480.14290.846616.931217.1791-12.3323
41.94090.67550.31291.26270.98424.67630.1634-0.16540.3234-0.218-0.1435-0.3115-0.40731.68890.01020.9842-0.23650.07031.41240.20651.083523.59518.5449-5.9999
57.8389-0.4413-4.034.31063.18724.3434-0.3530.1159-0.5211-0.35710.1130.84050.979-1.62890.47221.4117-0.32920.05531.16450.10520.917533.480342.327-12.6285
62.2958-0.3559-0.90263.4505-1.41774.0792-0.317-0.3173-0.6299-0.53120.1179-0.1661.49110.4441-0.03841.1495-0.02680.05431.016-0.01280.80346.936436.5229-23.6086
72.34851.02460.82712.4275-0.39126.6667-0.1340.3861-0.4008-0.34640.1339-0.09351.2527-0.2708-0.03461.0465-0.13870.06080.69310.00490.807446.107841.6528-27.444
81.7411-0.47240.20060.97052.3516.1444-0.13210.9271-0.1734-0.56940.07650.1910.55360.22450.05531.6567-0.27080.08640.8556-0.09190.884647.647542.0787-46.7566
90.37990.49160.80591.90952.4163.02290.05750.1925-0.3281-0.8331-0.76570.36560.2171-1.97710.23321.5-0.6072-0.04851.4864-0.03750.874236.336939.3778-44.0506
104.2568-3.00960.57913.7557-0.93715.350.08340.0121-0.7868-0.3888-0.31011.45191.3014-1.53140.22691.5617-0.6827-0.10311.438-0.05091.211931.632837.9013-37.179
111.8106-0.860.68811.2919-0.96710.86930.39890.7578-1.91380.3084-0.6809-0.1280.94320.0901-0.47681.497-0.1151-0.03631.2091-0.00351.13972.5757-25.947-20.7921
124.8913-2.69874.0374.0764-1.35623.78061.01820.0134-0.2796-0.4744-0.68981.210.55861.0049-0.33421.1575-0.62370.13081.0833-0.0721.153-9.9551-14.7358-17.5307
132.16410.04461.30392.8908-0.36853.03210.3306-0.0925-0.45620.4092-0.33150.41331.3945-0.69740.08961.5774-0.33590.13271.06840.05950.8976-3.9157-19.6797-6.8735
142.8406-0.61633.00451.14220.45694.3478-0.2121-0.01210.59590.08450.19290.7552-0.4023-2.03090.3211.1796-0.34050.21271.80310.02721.1324-14.4563-8.55664.951
150.5926-0.8398-0.01951.33360.14580.1156-0.4187-0.85440.21191.46130.5544-0.60680.4034-0.55270.43041.3016-0.70680.1951.33510.22150.7799-4.1546-11.944413.349
162.262-1.5319-2.66341.11251.55883.4745-0.9947-0.6719-0.5011-0.13180.6730.40450.0978-0.60910.22981.6644-0.45470.18651.70840.12440.795-7.0984-12.887416.9558
170.59980.6454-1.83040.7174-2.29016.94470.00550.41450.09030.5359-0.20010.21312.0729-1.2701-0.17692.2866-0.53650.1321.34510.28311.0797-2.7326-24.449910.9819
185.42792.83453.07873.09112.64232.3760.3277-0.229-0.71870.45180.13710.00133.5595-0.1236-0.17752.7001-0.3178-0.01271.40360.4511.37110.8996-30.63384.2826
190.8833-0.2529-0.92750.78330.83382.85330.59080.65191.6716-0.1849-0.5360.4645-1.4329-0.623-0.38021.7449-0.2090.02940.6135-0.00541.085654.234481.6848-52.0391
204.452.7416-3.16635.2446-2.0172.36750.1983-0.92280.3641-0.6466-0.4425-1.20180.53050.3205-0.51341.0057-0.3-0.00961.1943-0.09150.982766.253970.1673-48.757
211.4979-0.135-0.67691.14060.43466.03040.2903-0.5980.54280.2953-0.2064-0.3612-1.42951.5606-0.04451.3038-0.46860.01461.2342-0.05770.977162.043372.7366-34.4569
222.3731-1.1463.75081.4157-0.438.5179-0.2703-0.83480.66780.5214-0.1637-0.2301-0.64350.6155-0.0161.7459-0.5437-0.03041.5067-0.08431.005862.860872.3441-17.0209
23-0.00090.06790.09031.71552.16842.7301-0.3372-0.73410.27050.11540.020.136-2.58190.8053-0.17072.267-0.6870.08591.4323-0.24641.105457.590181.7137-20.0279
243.25740.756-3.38831.0484-1.32823.79590.06810.3620.86150.61360.21180.2439-2.7375-0.5329-0.33732.4821-0.42430.09241.2403-0.18931.426955.927486.317-26.9565
251.3675-1.5811-1.1524.68743.92733.577-0.04660.71280.381-0.9118-0.6167-0.18740.62430.75340.18331.751-0.0685-0.0550.71070.28831.075518.286233.1804-15.0951
264.1089-2.89584.69982.7028-3.47465.32120.6813-0.437-1.0209-1.72510.53030.21490.56211.5746-0.29291.1871-0.31560.14151.17570.24771.386331.805321.5341-6.6332
272.1027-2.8963-1.87754.01022.60843.52520.37940.2654-0.4185-1.3201-1.18771.6923-1.1266-0.70610.04722.7515-0.8312-0.14770.5779-0.67881.260936.641523.0267-46.2787
288.0651.85221.86882.95470.27022.06830.6635-0.41740.13-1.96351.0738-0.09520.7817-1.4751-0.55271.5536-0.8013-0.14251.6263-0.06671.180323.501634.8777-37.7775
293.1859-2.0781-0.30723.5248-2.54713.4758-0.186-0.5739-0.6745-0.5939-0.0136-0.41380.8810.58490.75471.9251-0.4625-0.10221.8282-0.37891.349572.827289.0579-18.783
302.4353-2.03741.57144.634-3.79823.23080.5536-1.5954-0.01710.2482-0.52770.23560.5871.4004-0.40462.2473-0.4151-0.12781.5119-0.35691.685261.667296.4203-18.9782
314.90161.87631.43261.3223-1.68168.61330.44631.0223-1.66480.72750.7977-0.56480.1635-0.0383-1.07462.05660.2656-0.23960.7783-0.08161.81846.636892.6836-32.0711
321.4331-1.5955-1.80081.85992.11132.3939-0.39270.52660.9214-1.1391-0.87140.398-2.52121.16760.4262.0955-0.58250.12251.80310.03291.5427-18.9118-33.810612.1647
339.3097-0.68190.64811.19690.30781.38442.063-2.1179-0.14910.8858-0.8196-0.24820.57960.0124-0.422.2844-0.48370.18510.97830.65111.7897-1.0136-39.20388.6997
341.99981.99992.00011.999921.9999-1.01550.5233-1.6792-0.47630.77261.7032-0.0004-0.64420.23411.12590.4495-0.18811.3608-0.59862.875516.4231-34.1252-4.5587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 271 )
4X-RAY DIFFRACTION4chain 'A' and (resid 272 through 299 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 31 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 68 )
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 199 )
8X-RAY DIFFRACTION8chain 'B' and (resid 200 through 254 )
9X-RAY DIFFRACTION9chain 'B' and (resid 255 through 271 )
10X-RAY DIFFRACTION10chain 'B' and (resid 272 through 299 )
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 31 )
12X-RAY DIFFRACTION12chain 'C' and (resid 32 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 172 )
14X-RAY DIFFRACTION14chain 'C' and (resid 173 through 199 )
15X-RAY DIFFRACTION15chain 'C' and (resid 200 through 215 )
16X-RAY DIFFRACTION16chain 'C' and (resid 216 through 238 )
17X-RAY DIFFRACTION17chain 'C' and (resid 239 through 271 )
18X-RAY DIFFRACTION18chain 'C' and (resid 272 through 299 )
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 31 )
20X-RAY DIFFRACTION20chain 'D' and (resid 32 through 48 )
21X-RAY DIFFRACTION21chain 'D' and (resid 49 through 215 )
22X-RAY DIFFRACTION22chain 'D' and (resid 216 through 254 )
23X-RAY DIFFRACTION23chain 'D' and (resid 255 through 271 )
24X-RAY DIFFRACTION24chain 'D' and (resid 272 through 299 )
25X-RAY DIFFRACTION25chain 'E' and (resid 61 through 70 )
26X-RAY DIFFRACTION26chain 'E' and (resid 71 through 81 )
27X-RAY DIFFRACTION27chain 'F' and (resid 61 through 70 )
28X-RAY DIFFRACTION28chain 'F' and (resid 71 through 81 )
29X-RAY DIFFRACTION29chain 'G' and (resid 62 through 66 )
30X-RAY DIFFRACTION30chain 'G' and (resid 67 through 76 )
31X-RAY DIFFRACTION31chain 'G' and (resid 77 through 81 )
32X-RAY DIFFRACTION32chain 'H' and (resid 61 through 65 )
33X-RAY DIFFRACTION33chain 'H' and (resid 66 through 80 )
34X-RAY DIFFRACTION34chain 'H' and (resid 81 through 81 )

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