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- PDB-5b8i: Crystal structure of Calcineurin A and Calcineurin B in complex w... -

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Basic information

Entry
Database: PDB / ID: 5b8i
TitleCrystal structure of Calcineurin A and Calcineurin B in complex with FKBP12 and FK506 from Coccidioides immitis RS
Components
  • Calcineurin subunit B, variant
  • Peptidylprolyl isomerase
  • Serine/threonine-protein phosphatase
KeywordsHYDROLASE / SSGCID / NIH / NIAID / SBRI / UW / BERYLLIUM / PHOSPHATASE / CALCINEURIN / FKBP12 / FK506 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / calcium-dependent protein serine/threonine phosphatase regulator activity / calmodulin-dependent protein phosphatase activity / calcineurin-mediated signaling / protein-serine/threonine phosphatase / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calmodulin binding / calcium ion binding
Similarity search - Function
Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Sas10 C-terminal domain / Sas10 C-terminal domain / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / EF hand / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. ...Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Sas10 C-terminal domain / Sas10 C-terminal domain / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / 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 / Purple Acid Phosphatase; chain A, domain 2 / Chitinase A; domain 3 - #40 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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 / Calcineurin regulatory subunit / Peptidylprolyl isomerase / Serine/threonine-protein phosphatase / Sas10/Utp3 family protein
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
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
DepositionMay 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Data collection
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 18, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / entity / struct_ref / struct_ref_seq / struct_ref_seq_dif
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.title / _citation.year / _entity.pdbx_description / _entity.pdbx_ec / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.5Nov 13, 2019Group: Database references / Category: citation / citation_author
Revision 1.6Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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
B: Calcineurin subunit B, variant
C: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,21723
Polymers79,0593
Non-polymers2,15920
Water12,376687
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.670, 154.630, 64.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsSize exclusion chromatography indicates trimer

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Serine/threonine-protein phosphatase


Mass: 45097.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus)
Strain: RS / Gene: CIMG_06667 / Plasmid: pEMB36 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: J3K9C5, UniProt: J3K8M7*PLUS
#2: Protein Calcineurin subunit B, variant


Mass: 19502.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus)
Strain: RS / Gene: CIMG_02704 / Plasmid: pEMB36 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0D8JSK0
#3: Protein Peptidylprolyl isomerase


Mass: 14458.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus)
Strain: RS / Gene: CIMG_08666 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: J3K5Z5, peptidylprolyl isomerase

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Non-polymers , 7 types, 707 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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 / Comment: medication*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: COCCIDIOIDES IMMITIS, COMPLEX NAMED COIMA.00174.A.GM11, AND COMPOSED OF CALCINEURIN A (COIMA.00174.A.GM11), CALCINEURIN B (COIMA.01011.A.GJ11), AND FKBP12 (COIMA.18272.A.GK11) PURIFIED IN ...Details: COCCIDIOIDES IMMITIS, COMPLEX NAMED COIMA.00174.A.GM11, AND COMPOSED OF CALCINEURIN A (COIMA.00174.A.GM11), CALCINEURIN B (COIMA.01011.A.GJ11), AND FKBP12 (COIMA.18272.A.GK11) PURIFIED IN THE PRESENCE OF FK506/ TACROLIMUS (PROTEIN BATCH #D00367) AT 10.81 MG/ML. PROTEIN BUFFER INCLUDES 25MM HEPES PH 8.0, 50 MM NACL, 5.0MM CACL2, 0.5MM TCEP, AND 5UM FK506. THE PROTEIN COMPLEX WAS CRYSTALLIZED AGAINST THE SPARSE MATRIX SCREEN PROPLEX V/V PROPANOL-1 AND CRYO-PROTECTED WITH 20% ETHYLENE GLYCOL; CRYSTAL TRACKING ID 261098D2 (HLC3-10), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 81827 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.39 % / Biso Wilson estimate: 26.54 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.7
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(PHENIX.REFINE: DEV_1932)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCO

1tco


Resolution: 1.85→45.27 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 15.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.172 4019 4.91 %
Rwork0.145 --
obs0.147 81815 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 126 687 5974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025516
X-RAY DIFFRACTIONf_angle_d1.6417476
X-RAY DIFFRACTIONf_dihedral_angle_d14.5612076
X-RAY DIFFRACTIONf_chiral_restr0.114804
X-RAY DIFFRACTIONf_plane_restr0.009966
LS refinement shellResolution: 1.85→1.8718 Å / Phase error: 16.55
RfactorNum. reflection% reflection
Rfree0.2025 133 -
Rwork0.1704 2644 -
obs--100 %
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)
11.67330.1122-0.80041.60230.36031.9429-0.04710.21650.0564-0.26170.14380.2309-0.0174-0.3655-0.09530.1002-0.0116-0.0360.20820.01820.188413.104637.789118.4316
20.8222-0.30930.16191.5888-0.181.41030.0159-0.0401-0.0156-0.0083-0.0270.06310.0657-0.04390.01530.0334-0.01260.00150.1008-0.00520.102128.013129.455925.3026
30.9116-0.47240.19421.9711-0.51331.6789-0.0002-0.05920.0771-0.04650.0158-0.0142-0.056-0.0033-0.01310.04620.01040.00740.0982-0.02380.080729.723737.334425.0956
41.8464-2.95350.5398.6302-0.75751.2333-0.0595-0.13540.02580.14560.1053-0.0020.0367-0.0258-0.03810.0197-0.01820.00430.1259-0.00770.071734.817631.495331.3823
51.8892-0.36550.2971.73350.18691.40890.0138-0.0528-0.0285-0.0318-0.0475-0.35640.07990.3201-0.02980.07940.0224-0.01020.1940.01760.205751.122427.617329.885
62.8944-0.43880.58151.7445-0.09192.22290.05350.1548-0.1325-0.2526-0.0401-0.21370.23920.2050.03820.13780.02120.03330.1327-0.03730.162642.406420.258518.071
70.7965-0.43690.20592.2351-1.06631.06490.07130.11820.1646-0.3059-0.0776-0.00250.0531-0.00020.01190.12330.02670.00570.12880.0070.098929.528845.85234.1597
84.1869-2.42632.98571.9931-2.97354.8168-0.0876-0.0952-0.20320.46820.1843-0.0647-0.1004-0.1556-0.09550.4697-0.0403-0.03390.16250.01870.249415.556786.3141-8.2338
92.11260.98531.60627.59836.68328.317-0.05340.1770.18260.0071-0.058-0.5089-0.55810.65190.12160.3543-0.0428-0.09590.21230.10120.307623.37183.5998-15.1852
106.3678-4.27342.36225.3639-2.03614.95430.10050.1682-0.2912-0.6819-0.2777-0.08860.60440.13010.21250.36280.0135-0.02260.14130.0210.209717.921772.1601-22.6482
112.9290.17260.70561.3675-1.56596.77460.22690.64460.3101-0.3157-0.4012-0.6455-0.14750.3860.16590.44260.13450.07990.32030.14090.362427.214863.3427-16.4468
128.6341-3.37893.91293.9309-5.3397.5151-0.0227-0.09330.25510.0331-0.1233-0.16730.33-0.20080.12840.2546-0.0278-0.0490.1273-0.01120.211814.913168.5004-12.0905
132.94380.40642.32612.10761.02118.5876-0.2201-0.13350.10420.5402-0.08-0.2047-0.41230.35060.29260.33850.0044-0.08340.16190.03180.251220.379977.8992-5.4357
143.81312.53181.10168.20271.98332.4502-0.1338-0.07370.20960.29760.02680.1864-0.5618-0.05610.11170.29320.0709-0.03990.190.07990.20918.920868.112.1112
152.8754-1.27820.41152.3121-0.80882.6840.2170.214-0.1033-0.57120.02220.4920.2104-0.4323-0.1850.26620.0311-0.1090.19250.05350.275716.817355.5117-3.5001
165.1510.7083-0.60015.72962.09847.4350.00040.0505-0.2016-0.34150.1330.44540.3725-0.4136-0.09150.19030.0029-0.06390.11850.05850.172120.707346.33023.8508
173.79283.4991-2.36364.0471-0.9193.81240.0933-0.5991-0.33630.57530.13320.624-0.3809-0.4949-0.19330.28130.09220.03120.30090.08690.325214.004159.743310.2529
181.7256-0.68170.65595.3429-5.15625.03380.05290.18680.61860.6202-0.4337-0.485-0.31041.10710.37430.4806-0.0455-0.13370.4130.03390.41528.344768.59114.9929
191.74340.0685-0.88360.03420.09230.9585-0.1185-0.2201-0.09050.0160.0525-0.07650.16090.1873-0.10860.38580.13710.27590.60940.19640.551254.134249.1223-3.2525
200.0348-0.04030.04270.0439-0.05660.0674-0.1107-0.0493-0.163-0.1275-0.0288-0.11220.15510.1929-0.0890.84950.09240.46470.37240.08380.391448.453748.0655-16.4963
213.01510.9252-0.38493.53881.16085.8572-0.2-0.196-0.1624-0.6404-0.157-0.41990.53180.54530.34340.37140.13550.16340.320.10780.290641.626946.706-2.3309
223.87761.55741.91164.33630.7692.7912-0.0381-0.4089-0.10750.1775-0.1251-0.91090.35410.62610.07240.3070.1026-0.01820.84890.19680.531350.837647.686510.9778
233.98532.09360.16814.58863.4555.3294-0.1996-0.3817-0.4447-0.2197-0.0511-0.35160.82750.17080.18130.37360.12570.09510.24820.05580.238836.466443.95280.1166
241.9044-0.7277-0.82540.73591.45173.4026-0.0308-0.11280.1482-0.4336-0.1185-0.497-0.10650.6353-0.11580.3330.0410.14890.26910.07210.32243.881555.3773-3.2776
251.6035-0.9627-0.91033.75534.67886.6363-0.3071-0.1299-0.1276-0.4398-0.0611-0.19260.34730.67130.19240.44910.03750.150.30320.0740.296243.792448.1868-4.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 75 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 143 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 189 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 216 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 290 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 291 through 343 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 344 through 388 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 16 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 30 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 44 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 54 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 71 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 87 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 88 through 99 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 100 through 123 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 124 through 140 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 141 through 157 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 158 through 168 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 11 through 18 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 19 through 30 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 31 through 40 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 41 through 54 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 55 through 64 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 65 through 109 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 110 through 130 )C0

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