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- PDB-5gn7: Crystal structure of alternative oxidase from Trypanosoma brucei ... -

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Basic information

Entry
Database: PDB / ID: 5gn7
TitleCrystal structure of alternative oxidase from Trypanosoma brucei brucei complexed with cumarin derivative-17
ComponentsAlternative oxidase, mitochondrial
KeywordsTRANSFERASE / Alternative oxidase / inhibitor / drug / African trypanosomes / OXIDO-REDUCTASE
Function / homology
Function and homology information


alternative oxidase activity / alternative respiration / Oxidoreductases / ferric iron binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Alternative oxidase / Alternative oxidase / Alternative oxidase superfamily / Alternative oxidase / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6XZ / : / HYDROXIDE ION / 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 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Dec 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 1.3Nov 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

Downloads & links

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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)151,45316
Polymers150,5734
Non-polymers88012
Water00
1
A: Alternative oxidase, mitochondrial
B: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9098
Polymers75,2872
Non-polymers6236
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-118 kcal/mol
Surface area23100 Å2
MethodPISA
2
C: Alternative oxidase, mitochondrial
D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5448
Polymers75,2872
Non-polymers2576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-134 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.312, 222.726, 63.165
Angle α, β, γ (deg.)90.00, 114.70, 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


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-6XZ / 4-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-7,8-bis(oxidanyl)chromen-2-one


Mass: 382.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22N2O5
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO

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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: 3.21 Å3/Da / Density % sol: 61.69 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.557
11H+4/2L, -K, -L20.443
ReflectionResolution: 3.2→50 Å / Num. obs: 31113 / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.59 / % possible all: 92.5

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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→45.54 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.915 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26839 1368 5.1 %RANDOM
Rwork0.19548 ---
obs0.19926 25522 86.45 %-
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--23.34 Å2-0 Å237.08 Å2
2---24.42 Å2-0 Å2
3---47.76 Å2
Refinement stepCycle: 1 / Resolution: 3.2→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 39 0 8623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198811
X-RAY DIFFRACTIONr_bond_other_d0.0030.028589
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.95711972
X-RAY DIFFRACTIONr_angle_other_deg1.1543.00119620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.96851052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97222.059408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.748151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.551596
X-RAY DIFFRACTIONr_chiral_restr0.0950.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022139
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_it5.7047.5214220
X-RAY DIFFRACTIONr_mcbond_other5.7047.5214219
X-RAY DIFFRACTIONr_mcangle_it8.99711.2555268
X-RAY DIFFRACTIONr_mcangle_other8.99611.2555269
X-RAY DIFFRACTIONr_scbond_it5.1017.8694590
X-RAY DIFFRACTIONr_scbond_other5.1017.8694591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.11611.6686705
X-RAY DIFFRACTIONr_long_range_B_refined12.41860.20410573
X-RAY DIFFRACTIONr_long_range_B_other12.41760.20810574
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
Rfree0.353 52 -
Rwork0.208 911 -
obs--42.74 %

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