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- PDB-6nli: 1.90 A resolution structure of WT BfrB from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 6nli
Title1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 11)
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION INHIBITOR
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Chem-KTM / Bacterioferritin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLovell, S. / Punchi-Hewage, A. / Battaile, K.P. / Yao, H. / Nammalwar, B. / Gnanasekaran, K.K. / Bunce, R.A. / Reitz, A.B. / Rivera, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI125529 United States
National Science Foundation (NSF, United States)MCB1615767 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity.
Authors: Punchi Hewage, A.N.D. / Yao, H. / Nammalwar, B. / Gnanasekaran, K.K. / Lovell, S. / Bunce, R.A. / Eshelman, K. / Phaniraj, S.M. / Lee, M.M. / Peterson, B.R. / Battaile, K.P. / Reitz, A.B. / Rivera, M.
History
DepositionJan 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,38444
Polymers222,96212
Non-polymers9,42232
Water23,4011299
1
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules

A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,76988
Polymers445,92424
Non-polymers18,84564
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area83560 Å2
ΔGint-200 kcal/mol
Surface area127280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.546, 194.227, 202.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-202-

HEM

21D-202-

HEM

31D-202-

HEM

41L-201-

HEM

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 5 or (resid 6...
21(chain B and (resid 1 through 5 or (resid 6...
31(chain C and (resid 1 through 5 or (resid 6...
41(chain D and (resid 1 through 5 or (resid 6...
51(chain E and (resid 1 through 5 or (resid 6...
61(chain F and (resid 1 through 5 or (resid 6...
71(chain G and (resid 1 through 38 or (resid 39...
81(chain H and (resid 1 through 5 or (resid 6...
91(chain I and (resid 1 through 4 or (resid 5...
101(chain J and (resid 1 through 4 or (resid 5...
111(chain K and (resid 1 or (resid 2 and (name...
121(chain L and (resid 1 or (resid 2 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and (resid 1 through 5 or (resid 6...AA1 - 51 - 5
12LYSLYSLYSLYS(chain A and (resid 1 through 5 or (resid 6...AA66
13METMETGLUGLU(chain A and (resid 1 through 5 or (resid 6...AA1 - 1561 - 156
14METMETGLUGLU(chain A and (resid 1 through 5 or (resid 6...AA1 - 1561 - 156
21METMETLYSLYS(chain B and (resid 1 through 5 or (resid 6...BB1 - 51 - 5
22LYSLYSLYSLYS(chain B and (resid 1 through 5 or (resid 6...BB66
23METMETGLUGLU(chain B and (resid 1 through 5 or (resid 6...BB1 - 1561 - 156
24METMETGLUGLU(chain B and (resid 1 through 5 or (resid 6...BB1 - 1561 - 156
31METMETLYSLYS(chain C and (resid 1 through 5 or (resid 6...CC1 - 51 - 5
32LYSLYSLYSLYS(chain C and (resid 1 through 5 or (resid 6...CC66
33METMETGLUGLU(chain C and (resid 1 through 5 or (resid 6...CC1 - 1561 - 156
34METMETGLUGLU(chain C and (resid 1 through 5 or (resid 6...CC1 - 1561 - 156
35METMETGLUGLU(chain C and (resid 1 through 5 or (resid 6...CC1 - 1561 - 156
36METMETGLUGLU(chain C and (resid 1 through 5 or (resid 6...CC1 - 1561 - 156
37METMETGLUGLU(chain C and (resid 1 through 5 or (resid 6...CC1 - 1561 - 156
41METMETLYSLYS(chain D and (resid 1 through 5 or (resid 6...DD1 - 51 - 5
42LYSLYSLYSLYS(chain D and (resid 1 through 5 or (resid 6...DD66
43METMETGLUGLU(chain D and (resid 1 through 5 or (resid 6...DD1 - 1561 - 156
44METMETGLUGLU(chain D and (resid 1 through 5 or (resid 6...DD1 - 1561 - 156
51METMETLYSLYS(chain E and (resid 1 through 5 or (resid 6...EE1 - 51 - 5
52LYSLYSLYSLYS(chain E and (resid 1 through 5 or (resid 6...EE66
53METMETGLUGLU(chain E and (resid 1 through 5 or (resid 6...EE1 - 1561 - 156
54METMETGLUGLU(chain E and (resid 1 through 5 or (resid 6...EE1 - 1561 - 156
61METMETLYSLYS(chain F and (resid 1 through 5 or (resid 6...FF1 - 51 - 5
62LYSLYSLYSLYS(chain F and (resid 1 through 5 or (resid 6...FF66
63METMETGLUGLU(chain F and (resid 1 through 5 or (resid 6...FF1 - 1561 - 156
64METMETGLUGLU(chain F and (resid 1 through 5 or (resid 6...FF1 - 1561 - 156
71METMETLYSLYS(chain G and (resid 1 through 38 or (resid 39...GG1 - 381 - 38
72ARGARGARGARG(chain G and (resid 1 through 38 or (resid 39...GG3939
73METMETGLUGLU(chain G and (resid 1 through 38 or (resid 39...GG1 - 1561 - 156
74METMETGLUGLU(chain G and (resid 1 through 38 or (resid 39...GG1 - 1561 - 156
75METMETGLUGLU(chain G and (resid 1 through 38 or (resid 39...GG1 - 1561 - 156
76METMETGLUGLU(chain G and (resid 1 through 38 or (resid 39...GG1 - 1561 - 156
77METMETGLUGLU(chain G and (resid 1 through 38 or (resid 39...GG1 - 1561 - 156
81METMETLYSLYS(chain H and (resid 1 through 5 or (resid 6...HH1 - 51 - 5
82LYSLYSLYSLYS(chain H and (resid 1 through 5 or (resid 6...HH66
83METMETGLUGLU(chain H and (resid 1 through 5 or (resid 6...HH1 - 1561 - 156
84METMETGLUGLU(chain H and (resid 1 through 5 or (resid 6...HH1 - 1561 - 156
85METMETGLUGLU(chain H and (resid 1 through 5 or (resid 6...HH1 - 1561 - 156
86METMETGLUGLU(chain H and (resid 1 through 5 or (resid 6...HH1 - 1561 - 156
87METMETGLUGLU(chain H and (resid 1 through 5 or (resid 6...HH1 - 1561 - 156
91METMETASPASP(chain I and (resid 1 through 4 or (resid 5...II1 - 41 - 4
92LYSLYSLYSLYS(chain I and (resid 1 through 4 or (resid 5...II5 - 65 - 6
93METMETGLUGLU(chain I and (resid 1 through 4 or (resid 5...II1 - 1561 - 156
94METMETGLUGLU(chain I and (resid 1 through 4 or (resid 5...II1 - 1561 - 156
95METMETGLUGLU(chain I and (resid 1 through 4 or (resid 5...II1 - 1561 - 156
96METMETGLUGLU(chain I and (resid 1 through 4 or (resid 5...II1 - 1561 - 156
97METMETGLUGLU(chain I and (resid 1 through 4 or (resid 5...II1 - 1561 - 156
101METMETASPASP(chain J and (resid 1 through 4 or (resid 5...JJ1 - 41 - 4
102LYSLYSLYSLYS(chain J and (resid 1 through 4 or (resid 5...JJ5 - 65 - 6
103METMETGLUGLU(chain J and (resid 1 through 4 or (resid 5...JJ1 - 1561 - 156
104METMETGLUGLU(chain J and (resid 1 through 4 or (resid 5...JJ1 - 1561 - 156
105METMETGLUGLU(chain J and (resid 1 through 4 or (resid 5...JJ1 - 1561 - 156
106METMETGLUGLU(chain J and (resid 1 through 4 or (resid 5...JJ1 - 1561 - 156
107METMETGLUGLU(chain J and (resid 1 through 4 or (resid 5...JJ1 - 1561 - 156
111METMETMETMET(chain K and (resid 1 or (resid 2 and (name...KK11
112LYSLYSLYSLYS(chain K and (resid 1 or (resid 2 and (name...KK22
113METMETGLUGLU(chain K and (resid 1 or (resid 2 and (name...KK1 - 1561 - 156
114METMETGLUGLU(chain K and (resid 1 or (resid 2 and (name...KK1 - 1561 - 156
115METMETGLUGLU(chain K and (resid 1 or (resid 2 and (name...KK1 - 1561 - 156
116METMETGLUGLU(chain K and (resid 1 or (resid 2 and (name...KK1 - 1561 - 156
121METMETMETMET(chain L and (resid 1 or (resid 2 and (name...LL11
122LYSLYSLYSLYS(chain L and (resid 1 or (resid 2 and (name...LL22
123METMETGLUGLU(chain L and (resid 1 or (resid 2 and (name...LL1 - 1561 - 156
124METMETGLUGLU(chain L and (resid 1 or (resid 2 and (name...LL1 - 1561 - 156
125METMETGLUGLU(chain L and (resid 1 or (resid 2 and (name...LL1 - 1561 - 156
126METMETGLUGLU(chain L and (resid 1 or (resid 2 and (name...LL1 - 1561 - 156

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Ferroxidase


Mass: 18580.168 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase

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Non-polymers , 5 types, 1331 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-KTM / 4-{[(2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 268.267 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H12N2O3
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1299 / 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: 2.86 Å3/Da / Density % sol: 57 % / Mosaicity: 0.1 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 30% (v/v) PEG 200, 0.1M sodium acetate, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.56 Å / Num. obs: 199628 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.8 / Num. measured all: 1337641 / Scaling rejects: 16
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.102 / Num. unique obs: 9820 / CC1/2: 0.757 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.31data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8O

5d8o


Resolution: 1.9→47.222 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.05
RfactorNum. reflection% reflection
Rfree0.2046 9934 4.98 %
Rwork0.1655 --
obs0.1675 199535 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.55 Å2 / Biso mean: 29.8047 Å2 / Biso min: 13.92 Å2
Refinement stepCycle: final / Resolution: 1.9→47.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15157 0 792 1299 17248
Biso mean--40.63 40.69 -
Num. residues----1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916456
X-RAY DIFFRACTIONf_angle_d0.94122292
X-RAY DIFFRACTIONf_chiral_restr0.0462354
X-RAY DIFFRACTIONf_plane_restr0.0062809
X-RAY DIFFRACTIONf_dihedral_angle_d17.7979659
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10878X-RAY DIFFRACTION3.417TORSIONAL
12B10878X-RAY DIFFRACTION3.417TORSIONAL
13C10878X-RAY DIFFRACTION3.417TORSIONAL
14D10878X-RAY DIFFRACTION3.417TORSIONAL
15E10878X-RAY DIFFRACTION3.417TORSIONAL
16F10878X-RAY DIFFRACTION3.417TORSIONAL
17G10878X-RAY DIFFRACTION3.417TORSIONAL
18H10878X-RAY DIFFRACTION3.417TORSIONAL
19I10878X-RAY DIFFRACTION3.417TORSIONAL
110J10878X-RAY DIFFRACTION3.417TORSIONAL
111K10878X-RAY DIFFRACTION3.417TORSIONAL
112L10878X-RAY DIFFRACTION3.417TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.29833460.250462816627100
1.9216-1.94420.3093110.241362646575100
1.9442-1.96790.25983140.224462816595100
1.9679-1.99280.27013440.220762656609100
1.9928-2.0190.2623480.208662706618100
2.019-2.04670.23653060.197263106616100
2.0467-2.07590.25093250.192662596584100
2.0759-2.10690.24243560.183562556611100
2.1069-2.13990.23953020.181762876589100
2.1399-2.17490.2343630.176462476610100
2.1749-2.21240.22953320.168562896621100
2.2124-2.25270.21983290.161563006629100
2.2527-2.2960.19932940.159363326626100
2.296-2.34290.20213430.159163136656100
2.3429-2.39380.20553320.157362496581100
2.3938-2.44950.21383290.154163056634100
2.4495-2.51070.19712980.152963246622100
2.5107-2.57860.1943130.147763286641100
2.5786-2.65450.20563080.150763766684100
2.6545-2.74020.19233580.152762556613100
2.7402-2.83810.18333100.147963456655100
2.8381-2.95170.21253410.150862906631100
2.9517-3.0860.19073550.164763496704100
3.086-3.24870.20793040.168963626666100
3.2487-3.45220.19163350.159963216656100
3.4522-3.71860.18363480.155663516699100
3.7186-4.09260.17523280.153163716699100
4.0926-4.68440.16873380.13564196757100
4.6844-5.90.21453720.176763946766100
5.9-47.23610.20743520.19126609696199

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