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- PDB-5b3q: Nqo5 of the trypsin-resistant fragment (1-134) in P63 form -

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Basic information

Entry
Database: PDB / ID: 5b3q
TitleNqo5 of the trypsin-resistant fragment (1-134) in P63 form
ComponentsNADH-quinone oxidoreductase subunit 5
KeywordsOXIDOREDUCTASE / NADH-ubiquinone oxidoreductase / complex I
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (ubiquinone) activity / quinone binding / plasma membrane
Similarity search - Function
NADH:ubiquinone oxidoreductase Nqo5 subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NADH-quinone oxidoreductase subunit 5
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsHanazono, Y. / Takeda, K. / Miki, K.
CitationJournal: Febs Open Bio / Year: 2016
Title: Characterization of the Nqo5 subunit of bacterial complex I in the isolated state
Authors: Hanazono, Y. / Takeda, K. / Miki, K.
History
DepositionMar 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-quinone oxidoreductase subunit 5


Theoretical massNumber of molelcules
Total (without water)15,6471
Polymers15,6471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.169, 55.169, 71.813
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein NADH-quinone oxidoreductase subunit 5 / NADH dehydrogenase I chain 5 / NDH-1 subunit 5


Mass: 15646.766 Da / Num. of mol.: 1 / Fragment: UNP residues 1-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: nqo5, TTHA0086 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56219, NADH dehydrogenase (quinone)

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 10% PEG 1000, 10% PEG 8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 2499 / % possible obs: 98.4 % / Redundancy: 8 % / Rsym value: 0.096 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 1.4 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3P

5b3p


Resolution: 3.003→39.778 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 24.6
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 111 4.45 %Random selection
Rwork0.1948 ---
obs0.1967 2494 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.003→39.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 0 0 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031120
X-RAY DIFFRACTIONf_angle_d0.761522
X-RAY DIFFRACTIONf_dihedral_angle_d13.072415
X-RAY DIFFRACTIONf_chiral_restr0.034155
X-RAY DIFFRACTIONf_plane_restr0.003201

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