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- PDB-5gn9: Crystal structure of alternative oxidase from Trypanosoma brucei ... -

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Basic information

Entry
Database: PDB / ID: 5gn9
TitleCrystal structure of alternative oxidase from Trypanosoma brucei brucei complexed with cumarin derivative-17b
ComponentsAlternative oxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Alternative oxidase / inhibitor / drug / African trypanosomes / TRANSFERASE
Function / homology
Function and homology information


alternative oxidase activity / Oxidoreductases / respirasome / ferric iron binding / mitochondrial inner membrane / oxidoreductase activity / mitochondrion
Similarity search - Function
Alternative oxidase / Alternative oxidase / Alternative oxidase superfamily / Alternative oxidase / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-butyl-7,8-bis(oxidanyl)chromen-2-one / : / Alternative oxidase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBalogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. ...Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. / Moore, A.L. / Harada, S. / Kita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japanese Society for the Promotion of Science26253025 Japan
CitationJournal: Faseb J. / Year: 2019
Title: Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase ofTrypanosoma brucei brucei.
Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. ...Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y.I. / Moore, A.L. / Harada, S. / Kita, K.
History
DepositionJul 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Alternative oxidase, mitochondrial
B: Alternative oxidase, mitochondrial
C: Alternative oxidase, mitochondrial
D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,95716
Polymers150,5734
Non-polymers1,38412
Water0
1
A: Alternative oxidase, mitochondrial
B: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9788
Polymers75,2872
Non-polymers6926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-100 kcal/mol
Surface area22480 Å2
MethodPISA
2
C: Alternative oxidase, mitochondrial
hetero molecules

D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9788
Polymers75,2872
Non-polymers6926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_548-x+1/2,y-1/2,-z+31
Buried area7870 Å2
ΔGint-96 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.218, 221.812, 62.611
Angle α, β, γ (deg.)90.00, 114.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Alternative oxidase, mitochondrial /


Mass: 37643.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: AOX / Production host: Escherichia coli (E. coli) / References: UniProt: Q26710, Oxidoreductases
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-6Y0 / 4-butyl-7,8-bis(oxidanyl)chromen-2-one


Mass: 234.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H14O4

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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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE
PH range: 7.3-7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 14, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.6
11H+4/2L, -K, -L20.4
ReflectionResolution: 3.2→50 Å / Num. obs: 32521 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.4
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.37 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VV9

3vv9


Resolution: 3.2→42.19 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 15.632 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25248 1418 5.1 %RANDOM
Rwork0.19157 ---
obs0.19472 26326 90.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.23 Å2-0 Å220.91 Å2
2---13.27 Å2-0 Å2
3---23.5 Å2
Refinement stepCycle: 1 / Resolution: 3.2→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 76 0 8660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198852
X-RAY DIFFRACTIONr_bond_other_d0.0020.028616
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.96112028
X-RAY DIFFRACTIONr_angle_other_deg1.1353.00219680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67851052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58222.059408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.094151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8251596
X-RAY DIFFRACTIONr_chiral_restr0.0990.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022144
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_it5.2436.8594220
X-RAY DIFFRACTIONr_mcbond_other5.2396.8594219
X-RAY DIFFRACTIONr_mcangle_it8.25410.2695268
X-RAY DIFFRACTIONr_mcangle_other8.25310.2695269
X-RAY DIFFRACTIONr_scbond_it4.9277.2664630
X-RAY DIFFRACTIONr_scbond_other4.9127.2654627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.87710.746756
X-RAY DIFFRACTIONr_long_range_B_refined11.63755.09610788
X-RAY DIFFRACTIONr_long_range_B_other11.63355.09910788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 68 -
Rwork0.226 1179 -
obs--56.2 %

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