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- PDB-4o9t: Mechanism of transhydrogenase coupling proton translocation and h... -

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Basic information

Entry
Database: PDB / ID: 4o9t
TitleMechanism of transhydrogenase coupling proton translocation and hydride transfer
Components
  • NAD(P) transhydrogenase subunit alpha 2
  • NAD(P) transhydrogenase subunit beta
KeywordsMEMBRANE PROTEIN / Nicotinamide nucleotide transhydrogenase couples the proton motive force to NADPH formation / Integral membrane component of Thermus thermophilus transhydrogenase / Respiratory enzyme / Protons and NAD(H) / NADP(H) / Proton translocation and hydride transfer / Periplasmic membrane and cytosol
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / oxidoreductase activity / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.079 Å
AuthorsLeung, J.H. / Yamaguchi, M. / Moeller, A. / Schurig-Briccio, L.A. / Gennis, R.B. / Potter, C.S. / Carragher, B. / Stout, C.D.
CitationJournal: Science / Year: 2015
Title: Structural biology. Division of labor in transhydrogenase by alternating proton translocation and hydride transfer.
Authors: Leung, J.H. / Schurig-Briccio, L.A. / Yamaguchi, M. / Moeller, A. / Speir, J.A. / Gennis, R.B. / Stout, C.D.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Structure summary
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta
C: NAD(P) transhydrogenase subunit alpha 2
D: NAD(P) transhydrogenase subunit beta
E: NAD(P) transhydrogenase subunit alpha 2
F: NAD(P) transhydrogenase subunit beta
G: NAD(P) transhydrogenase subunit alpha 2
H: NAD(P) transhydrogenase subunit beta


Theoretical massNumber of molelcules
Total (without water)160,6198
Polymers160,6198
Non-polymers00
Water00
1
A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta


Theoretical massNumber of molelcules
Total (without water)40,1552
Polymers40,1552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-86 kcal/mol
Surface area14950 Å2
MethodPISA
2
C: NAD(P) transhydrogenase subunit alpha 2
D: NAD(P) transhydrogenase subunit beta


Theoretical massNumber of molelcules
Total (without water)40,1552
Polymers40,1552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-82 kcal/mol
Surface area15060 Å2
MethodPISA
3
E: NAD(P) transhydrogenase subunit alpha 2
F: NAD(P) transhydrogenase subunit beta


Theoretical massNumber of molelcules
Total (without water)40,1552
Polymers40,1552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-87 kcal/mol
Surface area14900 Å2
MethodPISA
4
G: NAD(P) transhydrogenase subunit alpha 2
H: NAD(P) transhydrogenase subunit beta


Theoretical massNumber of molelcules
Total (without water)40,1552
Polymers40,1552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-83 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.221, 86.388, 125.149
Angle α, β, γ (deg.)90.00, 93.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NAD(P) transhydrogenase subunit alpha 2


Mass: 10649.571 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1779 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GR9, EC: 1.6.1.2
#2: Protein
NAD(P) transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta


Mass: 29505.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1778 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GS0, EC: 1.6.1.2

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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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 298 K / Method: lipidic subic phase / pH: 8.5
Details: 350 mM NH4-formate, 100mM Na-thiocynate, and 18% (v/v) 1-4-butanediol, pH 8.5, lipidic subic phase, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.079→46.3 Å / Num. obs: 36118 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.079→46.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.885 / SU B: 20.71 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27963 1899 5 %RANDOM
Rwork0.21945 ---
obs0.22249 36118 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.675 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å20 Å2-0.32 Å2
2---1.87 Å2-0 Å2
3----3.96 Å2
Refinement stepCycle: LAST / Resolution: 3.079→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10352 0 0 0 10352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910570
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210750
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.96314386
X-RAY DIFFRACTIONr_angle_other_deg0.9324484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30151400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66722.55298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.212151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7981530
X-RAY DIFFRACTIONr_chiral_restr0.0840.21760
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022392
X-RAY DIFFRACTIONr_mcbond_it4.7367.1885624
X-RAY DIFFRACTIONr_mcbond_other4.7297.1875623
X-RAY DIFFRACTIONr_mcangle_it7.47510.7647016
X-RAY DIFFRACTIONr_mcangle_other7.47510.7657017
X-RAY DIFFRACTIONr_scbond_it4.7987.8094946
X-RAY DIFFRACTIONr_scbond_other4.7987.814947
X-RAY DIFFRACTIONr_scangle_other7.46211.5157371
X-RAY DIFFRACTIONr_long_range_B_refined10.61759.94612935
X-RAY DIFFRACTIONr_long_range_B_other10.61659.9512936
LS refinement shellResolution: 3.079→3.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 118 -
Rwork0.322 2639 -
obs--98.36 %

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