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- PDB-5b3p: Nqo5 of the trypsin-resistant fragment (1-134) in P212121 form -

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Basic information

Entry
Database: PDB / ID: 5b3p
TitleNqo5 of the trypsin-resistant fragment (1-134) in P212121 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 / MAD / Resolution: 1.652 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-quinone oxidoreductase subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7674
Polymers15,6471
Non-polymers1203
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-16 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.264, 42.185, 70.095
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 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)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200mM calcium chloride, 25% PEG 4000

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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: 1.65→50 Å / Num. obs: 14331 / % possible obs: 93.8 % / Redundancy: 12.9 % / Rsym value: 0.052 / Net I/σ(I): 33.1
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 1.8 / % possible all: 70.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.652→29.498 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 712 4.98 %Random selection
Rwork0.1703 ---
obs0.1721 14289 93.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.652→29.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 3 120 1231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131172
X-RAY DIFFRACTIONf_angle_d1.5711601
X-RAY DIFFRACTIONf_dihedral_angle_d12.941449
X-RAY DIFFRACTIONf_chiral_restr0.078162
X-RAY DIFFRACTIONf_plane_restr0.009215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6517-1.77920.32811200.23322133X-RAY DIFFRACTION76
1.7792-1.95820.21591610.19132688X-RAY DIFFRACTION95
1.9582-2.24150.19431460.15932858X-RAY DIFFRACTION100
2.2415-2.82370.20951320.17192923X-RAY DIFFRACTION100
2.8237-29.5030.19691530.1622975X-RAY DIFFRACTION98

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