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- PDB-5zdq: Crystal structure of cyanide-insensitive alternative oxidase from... -

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Basic information

Entry
Database: PDB / ID: 5zdq
TitleCrystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with COLLETOCHLORIN B
ComponentsAlternative oxidase, mitochondrial
KeywordsMEMBRANE PROTEIN / MEMBRANE BOUND DIIRON PROTEIN
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
: / HYDROXIDE ION / Chem-RNB / Alternative oxidase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. ...Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. / Tanaka, A. / Inoue, M. / Saimoto, H. / Harada, S. / Moore, A.L. / Kita, K.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase.
Authors: Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. / Tanaka, A. / Inoue, M. / Saimoto, H. / Harada, S. / Moore, A.L. / Kita, K.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_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_comp_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
Revision 1.4Mar 19, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details
Item: _pdbx_database_related.db_id / _pdbx_database_related.details

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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)152,66323
Polymers150,5734
Non-polymers2,09019
Water5,278293
1
A: Alternative oxidase, mitochondrial
hetero molecules

A: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,38212
Polymers75,2872
Non-polymers1,09510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area8680 Å2
ΔGint-160 kcal/mol
Surface area22420 Å2
MethodPISA
2
B: Alternative oxidase, mitochondrial
C: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,19010
Polymers75,2872
Non-polymers9038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-115 kcal/mol
Surface area23470 Å2
MethodPISA
3
D: Alternative oxidase, mitochondrial
hetero molecules

D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,56614
Polymers75,2872
Non-polymers1,27912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9130 Å2
ΔGint-153 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.017, 137.920, 63.058
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-648-

HOH

21D-651-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): FN102 / References: UniProt: Q26710

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Non-polymers , 6 types, 312 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#4: Chemical
ChemComp-RNB / 3-chloro-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-4,6-dihydroxy-2-methylbenzaldehyde / Colletochlorin B


Mass: 322.826 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23ClO3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 30% PEG400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2012
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, L10.477
11H+4/2L, -K, -L20.523
ReflectionResolution: 2.3→50 Å / Num. obs: 82140 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4112 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VV9

3vv9


Resolution: 2.3→42.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.676 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21972 4048 4.9 %RANDOM
Rwork0.18472 ---
obs0.18648 77904 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.591 Å2
Baniso -1Baniso -2Baniso -3
1--25.07 Å2-0 Å2-2.45 Å2
2--31.55 Å20 Å2
3----6.48 Å2
Refinement stepCycle: 1 / Resolution: 2.3→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8608 0 116 293 9017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198916
X-RAY DIFFRACTIONr_bond_other_d0.0010.028690
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.96512113
X-RAY DIFFRACTIONr_angle_other_deg0.843319843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50651057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54222.098410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.351151531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9661596
X-RAY DIFFRACTIONr_chiral_restr0.0790.21379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022155
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 266 -
Rwork0.234 5615 -
obs--97.67 %

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