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- PDB-3jwq: Crystal structure of chimeric PDE5/PDE6 catalytic domain complexe... -

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Basic information

Entry
Database: PDB / ID: 3jwq
TitleCrystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil
ComponentscGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
KeywordsHYDROLASE / mostly alpha / Allosteric enzyme / cGMP / cGMP-binding / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein / Cell membrane / Lipoprotein / Membrane / Methylation / Prenylation / Sensory transduction / Vision
Function / homology
Function and homology information


positive regulation of oocyte development / retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / RHOBTB1 GTPase cycle / relaxation of cardiac muscle ...positive regulation of oocyte development / retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / RHOBTB1 GTPase cycle / relaxation of cardiac muscle / cGMP catabolic process / positive regulation of cardiac muscle hypertrophy / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / phototransduction, visible light / 3',5'-cyclic-GMP phosphodiesterase activity / Smooth Muscle Contraction / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / T cell proliferation / negative regulation of T cell proliferation / visual perception / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / GAF-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-VIA / cGMP-specific 3',5'-cyclic phosphodiesterase / Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsBarren, B. / Gakhar, L. / Muradov, H. / Boyd, K.K. / Ramaswamy, S. / Artemyev, N.O.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit
Authors: Barren, B. / Gakhar, L. / Muradov, H. / Boyd, K.K. / Ramaswamy, S. / Artemyev, N.O.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
B: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
C: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
D: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,38616
Polymers153,1284
Non-polymers2,25712
Water23413
1
A: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8464
Polymers38,2821
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8464
Polymers38,2821
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8464
Polymers38,2821
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8464
Polymers38,2821
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.732, 109.825, 199.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D
15A
25B
35C
45D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSER1AA537 - 6637 - 133
21THRTHRSERSER1BB537 - 6637 - 133
31THRTHRSERSER1CC537 - 6637 - 133
41THRTHRSERSER1DD537 - 6637 - 133
12TYRTYRHISHIS4AA664 - 678134 - 148
22TYRTYRHISHIS4BB664 - 678134 - 148
32TYRTYRHISHIS4CC664 - 678134 - 148
42TYRTYRHISHIS4DD664 - 678134 - 148
13SERSERTRPTRP1AA679 - 787149 - 257
23SERSERTRPTRP1BB679 - 787149 - 257
33SERSERTRPTRP1CC679 - 787149 - 257
43SERSERTRPTRP1DD679 - 787149 - 257
14GLUGLULYSLYS4AA788 - 815258 - 285
24GLUGLULYSLYS4BB788 - 815258 - 285
34GLUGLULYSLYS4CC788 - 815258 - 285
44GLUGLULYSLYS4DD788 - 815258 - 285
15LEULEUGLNGLN1AA816 - 859286 - 329
25LEULEUGLNGLN1BB816 - 859286 - 329
35LEULEUGLNGLN1CC816 - 859286 - 329
45LEULEUGLNGLN1DD816 - 859286 - 329

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera / cGMP-binding cGMP-specific phosphodiesterase / CGB-PDE / cGMP phosphodiesterase 6C


Mass: 38282.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE5A, PDE5, PDE6C, PDEA2 / Production host: Escherichia coli (E. coli)
References: UniProt: O76074, UniProt: P51160, 3',5'-cyclic-GMP phosphodiesterase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-VIA / 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE / SILDENAFIL / VIAGRA


Mass: 474.576 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H30N6O4S / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 200 mM MgSO4, 12% PEG-3350, 2.5% ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 23, 2006
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→29.8 Å / Num. all: 31941 / Num. obs: 31941 / % possible obs: 86.68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.873→2.947 Å / % possible all: 72.34

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H42

2h42


Resolution: 2.87→23.08 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / SU B: 35.246 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27528 1655 4.9 %RANDOM
Rwork0.22337 ---
all0.22588 31941 --
obs0.22588 31941 86.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.415 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--1.25 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.87→23.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10570 0 140 13 10723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.96614797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5151294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5124.618537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.705151996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8461564
X-RAY DIFFRACTIONr_chiral_restr0.1050.21650
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4331.56494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.961210492
X-RAY DIFFRACTIONr_scbond_it1.68834437
X-RAY DIFFRACTIONr_scangle_it2.9534.54305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1016TIGHT POSITIONAL0.050.05
1B1016TIGHT POSITIONAL0.050.05
1C1016TIGHT POSITIONAL0.050.05
1D1016TIGHT POSITIONAL0.040.05
1A1016TIGHT THERMAL0.110.5
1B1016TIGHT THERMAL0.10.5
1C1016TIGHT THERMAL0.090.5
1D1016TIGHT THERMAL0.090.5
2A130MEDIUM POSITIONAL0.580.5
2B130MEDIUM POSITIONAL0.520.5
2C130MEDIUM POSITIONAL0.780.5
2D130MEDIUM POSITIONAL0.630.5
2A130MEDIUM THERMAL0.722
2B130MEDIUM THERMAL0.782
2C130MEDIUM THERMAL0.732
2D130MEDIUM THERMAL0.582
3A892TIGHT POSITIONAL0.060.05
3B892TIGHT POSITIONAL0.070.05
3C892TIGHT POSITIONAL0.050.05
3D892TIGHT POSITIONAL0.060.05
3A892TIGHT THERMAL0.120.5
3B892TIGHT THERMAL0.120.5
3C892TIGHT THERMAL0.10.5
3D892TIGHT THERMAL0.10.5
4A233MEDIUM POSITIONAL0.660.5
4B233MEDIUM POSITIONAL0.740.5
4C233MEDIUM POSITIONAL0.730.5
4D233MEDIUM POSITIONAL0.880.5
4A233MEDIUM THERMAL0.72
4B233MEDIUM THERMAL0.752
4C233MEDIUM THERMAL0.822
4D233MEDIUM THERMAL0.812
5A358TIGHT POSITIONAL0.060.05
5B358TIGHT POSITIONAL0.060.05
5C358TIGHT POSITIONAL0.040.05
5D358TIGHT POSITIONAL0.050.05
5A358TIGHT THERMAL0.120.5
5B358TIGHT THERMAL0.110.5
5C358TIGHT THERMAL0.090.5
5D358TIGHT THERMAL0.10.5
LS refinement shellResolution: 2.873→2.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 102 -
Rwork0.378 1927 -
obs--72.34 %
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)
12.9166-1.3504-0.22252.7472-0.17211.46390.0002-0.0678-0.1105-0.1009-0.02290.16710.0658-0.2390.02260.081-0.0258-0.02040.156-0.02550.0747-24.981-21.14133.168
21.7679-0.35670.35561.45060.1640.61620.0254-0.1339-0.02870.17130.0031-0.1267-0.020.0346-0.02850.125-0.019-0.01640.1437-0.03170.0868-10.188-22.00939.962
33.33940.17272.462611.04430.04754.45460.0733-0.08450.68920.7444-0.1962-0.3259-0.13980.27330.1230.2329-0.15130.0480.3396-0.04240.339327.351-13.13415.575
41.6661-0.1246-0.27022.62410.55791.6283-0.0123-0.0579-0.05810.01970.053-0.02230.01530.0538-0.04070.07430.01360.01020.1948-0.00370.076915.957-29.09114.63
51.11510.4751.453954.161116.23146.45610.1967-0.4277-0.6594-1.33280.7823-0.99760.069-0.3271-0.9791.2271-0.39540.37110.39140.01471.2729-3.467-50.745-16.646
61.74070.74640.29122.66380.22682.3650.02910.1067-0.4356-0.1979-0.0399-0.06180.47580.0010.01090.39160.01940.02250.1432-0.02480.38680.303-68.3455.421
74.75740.0071-0.57216.63421.66844.5712-0.1480.0678-0.9050.24830.17420.3240.82090.1447-0.02610.5469-0.11010.04920.17050.12350.578-22.646-82.87144.618
81.71630.11390.22052.49220.39332.2494-0.0110.2035-0.1625-0.058-0.00980.27640.2684-0.20640.02070.2468-0.0335-0.03840.17070.08040.2495-17.518-63.61740.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A536 - 695
2X-RAY DIFFRACTION2A696 - 859
3X-RAY DIFFRACTION3B536 - 565
4X-RAY DIFFRACTION4B566 - 859
5X-RAY DIFFRACTION5C533 - 539
6X-RAY DIFFRACTION6C540 - 859
7X-RAY DIFFRACTION7D536 - 590
8X-RAY DIFFRACTION8D591 - 859

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