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- PDB-6tz7: Crystal Structure of Aspergillus fumigatus Calcineurin A, Calcine... -

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Basic information

Entry
Database: PDB / ID: 6tz7
TitleCrystal Structure of Aspergillus fumigatus Calcineurin A, Calcineurin B, FKBP12 and FK506 (Tacrolimus)
Components
  • Calcineurin Ca2+-binding regulatory subunit CnaB
  • FK506-binding protein 1A
  • Serine/threonine-protein phosphatase 2B catalytic subunit
KeywordsHydrolase/Isomerase/Calcium Binding / Calcineurin / FK506 / Hydrolase-Isomerase-Calcium Binding complex
Function / homology
Function and homology information


cellular response to pheromone / calcium-dependent protein serine/threonine phosphatase regulator activity / calcium-dependent protein serine/threonine phosphatase activity / calcineurin complex / fungal-type cell wall organization / intracellular monoatomic ion homeostasis / histone H2AXS140 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 ...cellular response to pheromone / calcium-dependent protein serine/threonine phosphatase regulator activity / calcium-dependent protein serine/threonine phosphatase activity / calcineurin complex / fungal-type cell wall organization / intracellular monoatomic ion homeostasis / histone H2AXS140 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 / myosin phosphatase activity / protein-serine/threonine phosphatase / calcineurin-mediated signaling / phosphatase binding / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / calmodulin binding / calcium ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / EF hand / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Chitinase A; domain 3 - #40 / Purple Acid Phosphatase; chain A, domain 2 ...Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / EF hand / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Chitinase A; domain 3 - #40 / Purple Acid Phosphatase; chain A, domain 2 / : / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Chitinase A; domain 3 / Metallo-dependent phosphatase-like / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / 4-Layer Sandwich / EF-hand domain pair / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / PHOSPHATE ION / Calcineurin subunit B / FK506-binding protein 1A / Serine/threonine-protein phosphatase 2B catalytic subunit
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFox III, D. / Horanyi, P.S.
Citation
Journal: Nat Commun / Year: 2019
Title: Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents.
Authors: Juvvadi, P.R. / Fox 3rd, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M.C. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. ...Authors: Juvvadi, P.R. / Fox 3rd, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M.C. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. / Trzoss, M. / Li, X. / Lee, S.C. / Chen, Y.L. / Mutz, M. / Spicer, L.D. / Schumacher, M.A. / Heitman, J. / Steinbach, W.J.
#1: Journal: Nat Commun / Year: 2019
Title: Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents
Authors: Juvvadi, P.R. / Fox III, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. / ...Authors: Juvvadi, P.R. / Fox III, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. / Trzoss, M. / Li, X. / Lee, S.C. / Chen, Y. / Mutz, M. / Spicer, L.D. / Schumacher, M.A. / Heitman, J. / Steinbach, W.J.
History
DepositionAug 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2B catalytic subunit
B: Calcineurin Ca2+-binding regulatory subunit CnaB
C: FK506-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,80812
Polymers78,5443
Non-polymers1,2659
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-146 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.240, 94.460, 69.830
Angle α, β, γ (deg.)90.00, 109.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Serine/threonine-protein phosphatase 2B catalytic subunit / Calmodulin-dependent calcineurin A subunit


Mass: 44895.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: cnaA, AFUA_5G09360 / Plasmid: PEMB361 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): TNI
References: UniProt: Q4WUR1, protein-serine/threonine phosphatase
#2: Protein Calcineurin Ca2+-binding regulatory subunit CnaB


Mass: 19692.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_6G04540 / Plasmid: PEMB361 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): TNI / References: UniProt: Q4WDF2
#3: Protein FK506-binding protein 1A / FKBP / Peptidyl-prolyl cis-trans isomerase / PPIase / Rapamycin-binding protein


Mass: 13956.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: fpr1A, AFUA_6G12170 / Plasmid: pEMB44 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4WLV6, peptidylprolyl isomerase

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Non-polymers , 7 types, 112 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: ASPERGILLUS FUMIGATUS VCID8013 [CALCINEURIN A], VCID8015 [CALCINEURIN B] AND VCID10288 [FKBP12] IN A SEC PURIFIED COMPLEX MEDIATED BY FK506/ TACROLIMUS AT 9.8 MG/ML [PROTEIN BATCH # 1393038]. ...Details: ASPERGILLUS FUMIGATUS VCID8013 [CALCINEURIN A], VCID8015 [CALCINEURIN B] AND VCID10288 [FKBP12] IN A SEC PURIFIED COMPLEX MEDIATED BY FK506/ TACROLIMUS AT 9.8 MG/ML [PROTEIN BATCH # 1393038]. PROTEIN BUFFER INCLUDES 25MM HEPES PH 8.0, 50 MM NACL, 5.0MM CACL2, AND 0.5MM TCEP. THE PROTEIN COMPLEX WAS CRYSTALLIZED AGAINST AN OPTIMIZATION SCREEN BASED ON THE SPARSE MATRIX SCREEN PACT CONDITION E9: 0.1M HEPES/NAOH, PH7.4, 0.2M POTASSIUM/SODIUM TARTRATE, 22.27% W/V PEG 3,350 AND CRYO-PROTECTED WITH 20% ETHYLENE GLYCOL
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 25206 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.112 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1860 / CC1/2: 0.728 / Rrim(I) all: 0.81 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1803refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCO

1tco


Resolution: 2.5→48.119 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.84
RfactorNum. reflection% reflection
Rfree0.232 1258 4.99 %
Rwork0.1995 --
obs0.2011 25187 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 75 103 4805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024834
X-RAY DIFFRACTIONf_angle_d0.5976574
X-RAY DIFFRACTIONf_dihedral_angle_d11.3411730
X-RAY DIFFRACTIONf_chiral_restr0.022716
X-RAY DIFFRACTIONf_plane_restr0.003852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.60010.29871282669
2.6001-2.71840.32611372654
2.7184-2.86170.31351412633
2.8617-3.0410.27931612621
3.041-3.27580.29931412660
3.2758-3.60530.25271282659
3.6053-4.12680.20641432658
4.1268-5.19830.17141360.15532657
5.19830.18591432718
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)
11.55571.5682-0.60913.27320.61371.10570.25840.05950.25740.4183-0.0520.33520.0247-0.2945-0.22660.3504-0.08160.04390.4558-0.01110.4839-22.0139-16.6774-21.8503
23.56922.3556-0.25545.9894-1.02483.64470.6631-0.34310.56150.7501-0.4090.7437-0.17330.0527-0.23190.3666-0.06490.11390.4081-0.0030.3246-31.3631-26.7474-27.5094
31.37540.2503-0.35692.62770.42262.64510.0353-0.0113-0.1104-0.155-0.1188-0.0229-0.05340.12580.07550.19840.03160.02680.22480.00550.2776-26.3035-33.3865-47.3503
41.1040.00050.23663.28141.70562.85420.06230.19120.1294-0.8164-0.02890.0772-0.5145-0.0511-0.02040.52220.04740.0320.28950.04560.2874-27.7069-25.7327-61.5077
55.1031-0.24082.77540.5319-0.00833.7202-0.1083-0.1902-0.1002-0.06920.04870.0198-0.2498-0.20710.12790.3815-0.0090.03550.21560.03020.4921-24.5017-17.3476-43.9109
60.1429-0.4151-0.24451.20350.69330.39940.2291-0.2329-0.38680.4749-0.2427-0.2784-0.2091.2054-0.24970.3399-0.1727-0.11260.60880.15250.357.6062-11.2449-30.3605
72.82810.10260.94920.8330.23770.5804-0.30350.15410.6573-0.09610.0457-0.0311-0.26910.27680.49750.8649-0.5602-0.26841.7182-0.05030.810128.7911-7.0659-18.6015
80.8108-0.0238-1.48282.2864-1.02664.10060.1253-0.01180.83510.0461-0.1434-0.2342-0.28930.83570.00240.7476-0.4277-0.23340.59040.15570.68389.2878-3.7311-22.6965
91.3404-0.15130.56984.8735-1.95220.97650.203-0.79530.48861.1544-0.26110.22920.01170.06650.18371.5318-0.1912-0.22751.0345-0.53340.805812.6374-3.0425-11.0591
103.9505-1.7982-0.91997.5623.07156.0093-0.0047-0.3174-0.0190.0967-0.60110.0051-0.86540.85520.50810.5-0.284-0.00911.29110.12820.411218.137-11.6932-17.7524
112.2790.35-0.76120.30940.4271.42070.0401-0.05110.03390.5815-0.0572-0.06560.35240.49260.06870.4873-0.0591-0.11260.54310.0390.50256.3882-15.7054-20.2016
124.0540.01421.2343.5519-0.56473.91480.0278-0.3537-0.22250.7889-0.05360.02250.0337-0.10730.06520.412-0.00650.01470.22570.02840.2791-6.1898-13.2476-23.0961
139.68221.85762.03351.1841.14744.6389-0.00721.3372-0.67520.04920.3658-0.00620.60370.717-0.53410.77090.2979-0.34340.6651-0.19010.6419.9215-20.3429-28.9458
142.9598-4.0166-2.58045.74042.12938.66310.8530.58690.5319-0.30740.29670.5757-0.23310.2999-1.0510.70920.17510.03030.4445-0.11470.842213.6278-18.8117-60.0266
155.1798-5.48426.08367.6551-4.97578.30590.38531.4778-0.1621-0.8416-0.4364-0.17010.55380.1845-0.13190.54090.07710.12770.6267-0.09050.44161.5585-9.1365-60.3262
163.0778-1.20530.45924.2317-0.71462.6220.12260.16470.4703-0.4369-0.2348-0.4644-0.39350.3010.10990.2602-0.02370.01820.2810.02310.20390.834-1.3803-51.1448
175.8206-1.8863-0.14549.49693.58664.3707-0.06610.048-0.11670.01850.00070.42310.5713-0.30760.03390.363-0.03120.0640.26560.040.4104-7.5908-16.4182-47.3536
185.26174.44842.77824.86651.32054.10930.1589-0.54440.64940.37250.0094-0.0304-0.0754-0.3781-0.14380.27920.0161-0.01040.35210.03770.31481.9379-4.1781-42.2513
192.2742-0.4760.89947.3228-0.86593.5140.10390.48740.1677-0.5903-0.2483-0.4249-0.08080.55960.07720.35040.00170.06320.3760.01460.3293.3832-6.4657-53.9009
201.1244-0.1096-0.57475.659-2.59913.13980.19760.063-0.35240.0285-0.2970.12440.15840.18090.11630.33620.00930.0510.31850.0070.41652.4649-16.1276-47.2581
217.7774-3.8933.66756.7171-2.23819.7047-0.1116-0.1815-0.3885-0.6052-0.34130.609-0.358-0.92140.51210.69520.08650.07160.4898-0.08490.3378-2.72127.9009-48.7586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 323 )
5X-RAY DIFFRACTION5chain 'A' and (resid 324 through 346 )
6X-RAY DIFFRACTION6chain 'A' and (resid 347 through 366 )
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 110 )
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 121 )
12X-RAY DIFFRACTION12chain 'B' and (resid 122 through 179 )
13X-RAY DIFFRACTION13chain 'B' and (resid 180 through 190 )
14X-RAY DIFFRACTION14chain 'C' and (resid -4 through 2 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 9 )
16X-RAY DIFFRACTION16chain 'C' and (resid 10 through 30 )
17X-RAY DIFFRACTION17chain 'C' and (resid 31 through 43 )
18X-RAY DIFFRACTION18chain 'C' and (resid 44 through 57 )
19X-RAY DIFFRACTION19chain 'C' and (resid 58 through 77 )
20X-RAY DIFFRACTION20chain 'C' and (resid 78 through 107 )
21X-RAY DIFFRACTION21chain 'C' and (resid 108 through 112 )

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