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- PDB-6ofd: The crystal structure of octadecyloxy(naphthalen-1-yl)methylphosp... -

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Basic information

Entry
Database: PDB / ID: 6ofd
TitleThe crystal structure of octadecyloxy(naphthalen-1-yl)methylphosphonic acid in complex with red kidney bean purple acid phosphatase
ComponentsFe(3+)-Zn(2+) purple acid phosphatase
KeywordsMETAL BINDING PROTEIN / Purple acid phosphatase / metallohydrolases / transition state / catalysis / osteoporosis
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region
Similarity search - Function
Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Chem-MF1 / TRIETHYLENE GLYCOL / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeder, D. / Schenk, G. / Guddat, L.W. / Hussein, W.M. / McGeary, R.P. / Kan, M.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP0986292 Australia
Australian Research Council (ARC)150104358 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis.
Authors: Feder, D. / Kan, M.W. / Hussein, W.M. / Guddat, L.W. / Schenk, G. / McGeary, R.P.
History
DepositionMar 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe(3+)-Zn(2+) purple acid phosphatase
B: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
C: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,83666
Polymers211,7064
Non-polymers12,13062
Water30,6071699
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25830 Å2
ΔGint-359 kcal/mol
Surface area63250 Å2
2
A: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,08733
Polymers105,8532
Non-polymers6,23531
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-177 kcal/mol
Surface area33620 Å2
MethodPISA
3
B: Fe(3+)-Zn(2+) purple acid phosphatase
C: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,74833
Polymers105,8532
Non-polymers5,89531
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-236 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.174, 126.174, 298.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1040-

HOH

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Components

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Protein , 1 types, 4 molecules ABDC

#1: Protein
Fe(3+)-Zn(2+) purple acid phosphatase / PAP / Iron(III)-zinc(II) purple acid phosphatase


Mass: 52926.434 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase

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Sugars , 6 types, 17 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4/a3-b1_a4-c1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 10 types, 1744 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-MF1 / [(S)-(naphthalen-1-yl)(octadecyloxy)methyl]phosphonic acid


Mass: 490.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C29H47O4P
#11: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#12: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: SO4
#13: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#14: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#15: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#16: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1699 / 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: 3.45 Å3/Da / Density % sol: 64.32 % / Description: Hexagonal
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4
Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20.05 Å / Num. obs: 139709 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rpim(I) all: 0.048 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.225 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4624 / CC1/2: 0.763 / Rpim(I) all: 0.293 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DHL

4dhl


Resolution: 2.2→20.045 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 18.04
RfactorNum. reflection% reflection
Rfree0.1994 6987 5.01 %
Rwork0.1552 --
obs0.1574 139525 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→20.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13988 0 737 1699 16424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815292
X-RAY DIFFRACTIONf_angle_d0.95120855
X-RAY DIFFRACTIONf_dihedral_angle_d5.86912034
X-RAY DIFFRACTIONf_chiral_restr0.0592205
X-RAY DIFFRACTIONf_plane_restr0.0052590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.29382470.22214377X-RAY DIFFRACTION100
2.225-2.25110.27562450.21874362X-RAY DIFFRACTION100
2.2511-2.27850.26962240.20884347X-RAY DIFFRACTION100
2.2785-2.30730.21122170.18254394X-RAY DIFFRACTION100
2.3073-2.33770.26932470.18274354X-RAY DIFFRACTION100
2.3377-2.36960.2442340.18364396X-RAY DIFFRACTION100
2.3696-2.40340.25232410.17624332X-RAY DIFFRACTION100
2.4034-2.43920.23552170.17534387X-RAY DIFFRACTION100
2.4392-2.47730.22252160.16774399X-RAY DIFFRACTION100
2.4773-2.51780.23262350.16624410X-RAY DIFFRACTION100
2.5178-2.56120.22472150.16864366X-RAY DIFFRACTION100
2.5612-2.60760.2292100.16954425X-RAY DIFFRACTION100
2.6076-2.65770.23492150.16514384X-RAY DIFFRACTION100
2.6577-2.71180.21922610.16914359X-RAY DIFFRACTION100
2.7118-2.77060.23022100.17384403X-RAY DIFFRACTION100
2.7706-2.83490.21792320.17064424X-RAY DIFFRACTION100
2.8349-2.90560.2282380.17334404X-RAY DIFFRACTION100
2.9056-2.98390.22082460.17394395X-RAY DIFFRACTION100
2.9839-3.07140.22772460.18294399X-RAY DIFFRACTION100
3.0714-3.17020.21512260.17044409X-RAY DIFFRACTION100
3.1702-3.2830.222280.17034388X-RAY DIFFRACTION100
3.283-3.41380.20282330.15194472X-RAY DIFFRACTION100
3.4138-3.56840.16512470.13564359X-RAY DIFFRACTION100
3.5684-3.75540.17082030.12534502X-RAY DIFFRACTION100
3.7554-3.98890.14812380.1214435X-RAY DIFFRACTION100
3.9889-4.29410.15682270.11614477X-RAY DIFFRACTION100
4.2941-4.72110.14742670.11194424X-RAY DIFFRACTION100
4.7211-5.39260.16392250.1264530X-RAY DIFFRACTION100
5.3926-6.75080.18862370.1554536X-RAY DIFFRACTION100
6.7508-20.04590.17952600.1764689X-RAY DIFFRACTION99

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