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- PDB-5doq: The structure of bd oxidase from Geobacillus thermodenitrificans -

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Basic information

Entry
Database: PDB / ID: 5doq
TitleThe structure of bd oxidase from Geobacillus thermodenitrificans
Components
  • Bd-type quinol oxidase subunit I
  • Bd-type quinol oxidase subunit II
  • Putative membrane protein
KeywordsOXIDOREDUCTASE / bd oxidase / terminal oxidase
Function / homology
Function and homology information


cytochrome complex / aerobic electron transport chain / electron transfer activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / CydS-like protein / Cytochrome ubiquinol oxidase subunit 1 / Cytochrome ubiquinol oxidase subunit 2 / Cytochrome bd terminal oxidase subunit I / Cytochrome bd terminal oxidase subunit II
Similarity search - Domain/homology
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME B/C / Putative membrane protein / Bd-type quinol oxidase subunit I / Bd-type quinol oxidase subunit II
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
Geobacillus sp. PA-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 Å
AuthorsSafarian, S. / Mueller, H. / Rajendran, C. / Preu, J. / Ovchinnikov, S. / Kusumoto, T. / Hirose, T. / Langer, J. / Sakamoto, J. / Michel, H.
CitationJournal: Science / Year: 2016
Title: Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases.
Authors: Safarian, S. / Rajendran, C. / Muller, H. / Preu, J. / Langer, J.D. / Ovchinnikov, S. / Hirose, T. / Kusumoto, T. / Sakamoto, J. / Michel, H.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / 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 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bd-type quinol oxidase subunit I
B: Bd-type quinol oxidase subunit II
C: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8106
Polymers92,9413
Non-polymers1,8693
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-146 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.060, 120.860, 122.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bd-type quinol oxidase subunit I


Mass: 50241.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / References: UniProt: A4IKP6
#2: Protein Bd-type quinol oxidase subunit II


Mass: 39017.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / References: UniProt: A4IKP7
#3: Protein/peptide Putative membrane protein


Mass: 3681.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus sp. PA-3 (bacteria) / References: UniProt: A0A0Q0UXS2
#4: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 400, Ammonium sulfate, Na-HEPES / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.73829 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73829 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 18373 / % possible obs: 56.7 % / Redundancy: 31.44 % / Rmerge(I) obs: 0.099 / Rsym value: 0.097 / Net I/σ(I): 19.17
Reflection shellResolution: 3.05→3.12 Å / Redundancy: 19.15 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 3.03 / % possible all: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.05→20 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.873 / SU B: 36.631 / SU ML: 0.588 / Cross valid method: THROUGHOUT / ESU R Free: 0.763 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.33472 897 4.9 %RANDOM
Rwork0.3194 ---
obs0.32015 17360 57.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6343 0 130 0 6473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196693
X-RAY DIFFRACTIONr_bond_other_d0.0010.026517
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9729191
X-RAY DIFFRACTIONr_angle_other_deg0.733314681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.135789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82222.299261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.088151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9661527
X-RAY DIFFRACTIONr_chiral_restr0.0530.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021623
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: 3.045→3.122 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.182 1 -
Rwork0.614 66 -
obs--2.95 %

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