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- PDB-5c8w: PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) ... -

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Basic information

Entry
Database: PDB / ID: 5c8w
TitlePKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cGMP
ComponentscGMP-dependent protein kinase 2
KeywordsTRANSFERASE / Binding Sites / Cyclic AMP / Cyclic GMP / Cyclic GMP-Dependent Protein Kinase Type II / Mutagenesis / Site-Directed / Protein Binding
Function / homology
Function and homology information


negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / positive regulation of protein localization / cGMP effects / cGMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation ...negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / positive regulation of protein localization / cGMP effects / cGMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / protein localization to plasma membrane / RAS processing / Ca2+ pathway / nuclear membrane / protein kinase activity / apical plasma membrane / protein phosphorylation / protein serine kinase activity / signal transduction / ATP binding / identical protein binding / cytosol
Similarity search - Function
cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Jelly Rolls / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
MALONIC ACID / CYCLIC GUANOSINE MONOPHOSPHATE / cGMP-dependent protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCampbell, J.C. / Reger, A.S. / Huang, G.Y. / Sankaran, B. / Kim, J.J. / Kim, C.W.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II.
Authors: Campbell, J.C. / Kim, J.J. / Li, K.Y. / Huang, G.Y. / Reger, A.S. / Matsuda, S. / Sankaran, B. / Link, T.M. / Yuasa, K. / Ladbury, J.E. / Casteel, D.E. / Kim, C.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 2
B: cGMP-dependent protein kinase 2
C: cGMP-dependent protein kinase 2
D: cGMP-dependent protein kinase 2
E: cGMP-dependent protein kinase 2
F: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,33022
Polymers99,4626
Non-polymers2,86916
Water12,827712
1
A: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0494
Polymers16,5771
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1304
Polymers16,5771
Non-polymers5533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0494
Polymers16,5771
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0263
Polymers16,5771
Non-polymers4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0263
Polymers16,5771
Non-polymers4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0494
Polymers16,5771
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.710, 103.454, 176.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
cGMP-dependent protein kinase 2 / cGK2 / cGMP-dependent protein kinase II / cGKII


Mass: 16576.941 Da / Num. of mol.: 6 / Fragment: unp residues 137-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG2, PRKGR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13237, cGMP-dependent protein kinase
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N5O7P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 33 mM cGMP, 200 mM sodium malonate, 5-10% ethylene glycol, 20% PEG

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.8→51.727 Å / Num. obs: 79944 / % possible obs: 99.63 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C8W

Resolution: 1.8→51.727 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 2000 2.5 %
Rwork0.1621 --
obs0.163 79940 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→51.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 190 712 6575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135967
X-RAY DIFFRACTIONf_angle_d1.488076
X-RAY DIFFRACTIONf_dihedral_angle_d13.7962173
X-RAY DIFFRACTIONf_chiral_restr0.106908
X-RAY DIFFRACTIONf_plane_restr0.0061010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.281340.23325199X-RAY DIFFRACTION95
1.845-1.89490.28751400.20935508X-RAY DIFFRACTION100
1.8949-1.95070.22221430.18925543X-RAY DIFFRACTION100
1.9507-2.01360.23481410.17775501X-RAY DIFFRACTION100
2.0136-2.08560.17951420.16915500X-RAY DIFFRACTION100
2.0856-2.16910.19721420.16355551X-RAY DIFFRACTION100
2.1691-2.26780.21151430.16495553X-RAY DIFFRACTION100
2.2678-2.38740.21651410.15985545X-RAY DIFFRACTION100
2.3874-2.5370.23121440.16815567X-RAY DIFFRACTION100
2.537-2.73290.20411440.17615617X-RAY DIFFRACTION100
2.7329-3.00790.20191420.16945566X-RAY DIFFRACTION100
3.0079-3.4430.23221460.16385666X-RAY DIFFRACTION100
3.443-4.33750.1571460.13225689X-RAY DIFFRACTION100
4.3375-51.74830.14981520.15135935X-RAY DIFFRACTION100
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)
13.0776-0.45670.03162.908-0.18576.5927-0.16070.10990.51040.01860.28810.6052-0.5163-0.2212-0.18970.1726-0.016-0.00150.13610.10750.3001-2.3996-0.4841-10.5341
22.5307-0.1624-0.68383.08123.49085.77410.03970.13520.40080.01840.09520.2445-0.564-0.0076-0.11270.1932-0.0180.02540.11560.07120.22655.1542.9399-11.1784
35.87065.23382.44314.65932.16131.0154-0.36130.3867-0.1537-0.49610.3337-0.0385-0.0301-0.06210.00910.1948-0.03220.05640.18810.0370.12684.4137-11.6922-19.5163
42.01050.5246-0.33052.6596-0.93122.2306-0.09970.2021-0.077-0.290.0977-0.06680.24-0.04270.01340.1524-0.01350.02020.11320.01470.10390.3353-19.1451-12.8387
56.2789-4.21880.58589.9634-0.83913.9161-0.12810.1594-0.26330.220.4578-0.08040.43840.0267-0.00640.2147-0.059-0.00540.1431-0.00090.1606-7.2091-26.0334-6.208
61.93640.1528-0.48592.5374-0.73651.3138-0.09420.01940.14850.02810.0561-0.07410.0137-0.03730.00790.1291-0.01110.00320.09350.01910.1119-0.2742-15.348-8.5157
73.77622.49451.74934.41841.5333.4678-0.08640.21160.24780.12160.0727-0.0742-0.2180.2134-0.00930.1491-0.03110.02010.12380.04110.12688.8137-5.1659-10.0465
85.2131-0.40090.79393.89170.19555.9325-0.1407-0.4092-0.06960.4055-0.06450.14370.1356-0.20420.18020.15870.01320.02770.1451-0.03980.15693.751-5.871322.739
96.8059-1.86432.44672.04020.71617.7604-0.09370.46960.6916-0.35230.0425-0.2428-0.51370.311-0.02190.2295-0.01370.02210.18760.03350.22342.8611-2.00147.7154
104.53881.6269-0.95567.0015-4.1124.78440.0753-0.18880.42030.2611-0.22030.2439-0.2867-0.07040.09160.18770.00960.01360.1662-0.05260.2201-2.6275-0.182218.0495
112.2936-2.6793-0.84733.16631.10470.5744-0.2308-0.2992-0.04070.41930.24330.14250.24130.11290.05570.22540.04640.04940.1668-0.01190.1662-3.2775-16.093822.3598
121.7272-0.3392.36261.5209-1.10885.3804-0.053-0.286-0.09730.19330.06320.17890.4049-0.2695-0.07920.1984-0.00910.03930.1714-0.00030.139-3.8149-24.884613.2378
130.51440.15950.37550.70790.71841.923-0.0207-0.1155-0.01690.06390.1282-0.06250.16180.2182-0.10210.17380.01350.00370.15180.00820.11053.7788-20.18114.6703
144.42884.51343.84884.59933.92583.36390.1765-0.0709-0.08690.50840.08860.04040.3066-0.1503-0.1840.21880.0504-0.01290.1308-0.00930.1437.6709-27.91635.9407
151.5761.70810.31792.93541.87962.3393-0.05280.05320.2451-0.1586-0.00860.2012-0.0846-0.04320.0550.1550.01180.00480.1197-0.00310.13410.2934-14.79868.5841
161.7297-0.77292.9040.5325-1.95377.18720.0272-0.0879-0.23980.27310.0289-0.15450.4120.1788-0.00850.24970.0365-0.00310.11750.03230.13014.0772-26.431317.072
174.6277-2.8691.02026.3626-0.95712.1282-0.0113-0.0482-0.0178-0.0075-0.02880.4207-0.0141-0.21030.12920.1408-0.00230.01310.1397-0.03640.1-6.2835-9.108615.1884
183.5282-0.05390.26835.2054-0.64463.70210.0734-0.04930.33950.2697-0.2013-0.0825-0.15910.43330.09680.1694-0.05370.02930.20680.01410.179627.78440.0739-15.0261
191.1507-0.5752-0.57252.8861.94112.3906-0.02970.01150.140.06320.0219-0.0452-0.01730.0799-0.00920.1676-0.06110.01480.19610.03180.174420.929-3.008-14.8663
200.3186-0.61030.84844.7038-2.85253.01820.12730.0512-0.0824-0.39980.06740.27980.3-0.2845-0.17460.1641-0.0456-0.01880.25720.06210.171119.9545-9.3621-33.4305
212.1912-0.8242-0.61461.9446-0.74933.33160.12780.48770.1192-0.2991-0.2103-0.14530.15190.07250.07430.1871-0.00120.02490.27310.07520.154428.4652-6.6079-32.5566
221.6196-0.39920.04181.5111-0.36292.22060.04420.14620.1976-0.0459-0.0602-0.0046-0.1146-0.04980.04550.1549-0.04250.0130.21960.08350.144224.6672-2.7325-29.4678
232.9838-1.9999-1.11283.01771.69442.416-0.00020.22090.4354-0.0874-0.024-0.0658-0.1447-0.1346-0.01530.1732-0.0646-0.00230.15450.09850.194616.77110.3506-18.8311
244.47880.5043-0.05692.16010.20654.7197-0.01630.2995-0.2916-0.25850.1958-0.27270.18910.16070.01760.18580.0273-0.01110.1506-0.06520.230119.6726-9.166515.807
252.50122.11440.56625.0578-0.2184.02140.0066-0.01630.5890.1366-0.22320.2312-0.7764-0.4207-0.07320.29410.0691-0.0130.1461-0.03350.343820.18154.878621.8033
266.6573-2.47880.40162.689-3.05434.8997-0.02080.796-0.0816-0.1691-0.1213-0.1142-0.07240.24050.07020.1691-0.001900.2338-0.02720.184626.6046-2.33914.2472
273.22662.6271-3.59283.6178-3.98017.155-0.0199-0.3373-0.92950.0832-0.0833-0.20750.4144-0.1047-0.03140.19580.01980.02790.12680.03650.317727.4779-14.357525.6784
282.12991.3748-0.49363.63511.03281.66250.1902-1.2553-0.76690.73270.1166-0.32560.1657-0.0631-0.10670.2299-0.0566-0.10230.45940.14450.260927.6198-10.971237.7139
291.762-0.356-1.45091.30610.28895.38250.3046-1.0937-0.28540.4721-0.1321-0.05570.2306-0.2805-0.10370.2589-0.09270.00090.44230.03350.16818.8297-8.978335.7986
304.46510.55681.80872.29930.82373.8371-0.0499-0.49850.16390.0084-0.11-0.0228-0.17880.05060.15350.1491-0.0033-0.00340.1829-0.03120.137923.6774-2.045131.7298
312.85242.14160.98055.51731.9491.67530.2286-0.9721-0.66390.602-0.12010.10010.4089-0.0604-0.04370.2989-0.0964-0.04170.33630.21410.314419.616-15.383836.7391
326.11442.5549-1.19754.9386-2.43774.9218-0.0954-0.1627-0.1582-0.00850.0156-0.2379-0.15350.30670.0190.14570.02270.00480.098-0.04680.157330.1507-4.741223.4354
335.5679-0.83831.11246.9609-0.71815.5830.0971-0.13280.61060.5773-0.18630.3669-0.3376-0.36980.05060.1904-0.02980.07740.2840.04570.455720.740524.7878-28.6708
342.1610.15361.2571.9684-0.5364.80970.06710.17050.83980.03810.08980.0134-0.2095-0.0838-0.02140.2261-0.05960.05140.23850.10050.47427.828826.6126-32.7631
351.3997-0.20580.24213.46030.63091.68490.10820.5590.4037-0.4326-0.1477-0.08780.0868-0.1677-0.01530.2297-0.00950.02410.38850.15090.252922.359413.9359-42.3345
363.4357-0.47592.94932.5133-0.30685.47710.07090.28750.50220.22160.095-0.2785-0.06410.2394-0.05930.1953-0.0690.02240.25350.1530.511831.706521.8089-32.4519
375.4047-0.439-0.39221.59241.67836.12280.10330.1915-0.0648-0.2815-0.20190.03940.2626-0.37360.15170.29640.0226-0.00620.2298-0.01240.4055-1.9171-22.124-59.6625
382.05030.1061-0.16253.04880.23652.98450.1724-0.2699-0.21460.2726-0.0831-0.21920.09370.2135-0.07870.25010.02230.02930.33920.10230.3128-0.9159-13.6954-44.0636
392.8725-0.665-3.54720.38771.23757.01960.0679-0.22790.25320.14590.3651-0.23290.35420.3802-0.43650.27380.0578-0.00720.17460.0130.47886.5929-19.6634-54.2187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 150 through 173 )
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 189 )
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 251 )
7X-RAY DIFFRACTION7chain 'A' and (resid 252 through 269 )
8X-RAY DIFFRACTION8chain 'B' and (resid 147 through 165 )
9X-RAY DIFFRACTION9chain 'B' and (resid 166 through 173 )
10X-RAY DIFFRACTION10chain 'B' and (resid 174 through 183 )
11X-RAY DIFFRACTION11chain 'B' and (resid 184 through 189 )
12X-RAY DIFFRACTION12chain 'B' and (resid 190 through 203 )
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 217 )
14X-RAY DIFFRACTION14chain 'B' and (resid 218 through 224 )
15X-RAY DIFFRACTION15chain 'B' and (resid 225 through 244 )
16X-RAY DIFFRACTION16chain 'B' and (resid 245 through 251 )
17X-RAY DIFFRACTION17chain 'B' and (resid 252 through 267 )
18X-RAY DIFFRACTION18chain 'C' and (resid 149 through 173 )
19X-RAY DIFFRACTION19chain 'C' and (resid 174 through 189 )
20X-RAY DIFFRACTION20chain 'C' and (resid 190 through 203 )
21X-RAY DIFFRACTION21chain 'C' and (resid 204 through 224 )
22X-RAY DIFFRACTION22chain 'C' and (resid 225 through 251 )
23X-RAY DIFFRACTION23chain 'C' and (resid 252 through 269 )
24X-RAY DIFFRACTION24chain 'D' and (resid 149 through 164 )
25X-RAY DIFFRACTION25chain 'D' and (resid 165 through 173 )
26X-RAY DIFFRACTION26chain 'D' and (resid 174 through 183 )
27X-RAY DIFFRACTION27chain 'D' and (resid 184 through 189 )
28X-RAY DIFFRACTION28chain 'D' and (resid 190 through 203 )
29X-RAY DIFFRACTION29chain 'D' and (resid 204 through 224 )
30X-RAY DIFFRACTION30chain 'D' and (resid 225 through 244 )
31X-RAY DIFFRACTION31chain 'D' and (resid 245 through 251 )
32X-RAY DIFFRACTION32chain 'D' and (resid 252 through 267 )
33X-RAY DIFFRACTION33chain 'E' and (resid 150 through 173 )
34X-RAY DIFFRACTION34chain 'E' and (resid 174 through 189 )
35X-RAY DIFFRACTION35chain 'E' and (resid 190 through 251 )
36X-RAY DIFFRACTION36chain 'E' and (resid 252 through 268 )
37X-RAY DIFFRACTION37chain 'F' and (resid 151 through 183 )
38X-RAY DIFFRACTION38chain 'F' and (resid 184 through 251 )
39X-RAY DIFFRACTION39chain 'F' and (resid 252 through 268 )

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