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

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Basic information

Entry
Database: PDB / ID: 5zdp
TitleCrystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ferulenol
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
Chem-9AU / : / HYDROXIDE ION / OXYGEN MOLECULE / Alternative oxidase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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 / struct_conn / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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 / _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

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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)152,68224
Polymers150,5734
Non-polymers2,10920
Water1,26170
1
A: Alternative oxidase, mitochondrial
B: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,34112
Polymers75,2872
Non-polymers1,05410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alternative oxidase, mitochondrial
hetero molecules

C: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,34112
Polymers75,2872
Non-polymers1,05410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
3
D: Alternative oxidase, mitochondrial
hetero molecules

D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,34112
Polymers75,2872
Non-polymers1,05410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Unit cell
Length a, b, c (Å)259.501, 63.109, 138.273
Angle α, β, γ (deg.)90.00, 122.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-607-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 2 / Auth seq-ID: 33 - 601 / Label seq-ID: 33

Dom-IDAuth asym-IDLabel asym-ID
1AA - Y
2BB - Z
3CC - AA
4DD - BA

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.428421, -0.000209, -0.903579), (-0.000311, -1, 0.000379), (-0.903579, 0.000443, 0.428421)463.88907, 64.87191, 293.46185
3given(-0.544221, -0.547006, -0.636088), (-0.757901, -0.004549, 0.652354), (-0.359735, 0.837117, -0.4121)420.42761, 96.98571, 241.64961
4given(0.810585, 0.542757, 0.219925), (-0.264372, 0.004049, 0.964412), (0.522551, -0.83988, 0.146772)-54.86688, -63.38938, 9.64943

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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 , 5 types, 90 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-9AU / 4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one


Mass: 366.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
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 MX300HE / Detector: CCD / Date: Jul 1, 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, L10.539
11H+4/2L, -K, -L20.461
ReflectionResolution: 2.7→50 Å / Num. obs: 52186 / % possible obs: 98.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2576 / % possible all: 98.5

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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: 2.71→39.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.263 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24852 2516 5.2 %RANDOM
Rwork0.1921 ---
obs0.195 45731 92.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.215 Å2
Baniso -1Baniso -2Baniso -3
1--17.89 Å2-0 Å2-1.45 Å2
2---0.89 Å2-0 Å2
3---18.78 Å2
Refinement stepCycle: 1 / Resolution: 2.71→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8598 0 128 70 8796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198912
X-RAY DIFFRACTIONr_bond_other_d0.0020.028694
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.96612098
X-RAY DIFFRACTIONr_angle_other_deg0.869319846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08951054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73522.059408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.104151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5031596
X-RAY DIFFRACTIONr_chiral_restr0.0760.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219854
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022174
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
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2759medium positional0.60.5
B2759medium positional0.580.5
C2759medium positional0.550.5
D2759medium positional0.570.5
A1549tight thermal12.450.5
B1549tight thermal12.750.5
C1549tight thermal10.740.5
D1549tight thermal16.160.5
A2759medium thermal12.72
B2759medium thermal12.892
C2759medium thermal11.272
D2759medium thermal17.12
LS refinement shellResolution: 2.706→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 87 -
Rwork0.205 1814 -
obs--50.07 %

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