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- PDB-4o93: Crystal structure of Thermus thermophilis transhydrogeanse domain... -

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Basic information

Entry
Database: PDB / ID: 4o93
TitleCrystal structure of Thermus thermophilis transhydrogeanse domain II dimer
Components
  • NAD(P) transhydrogenase subunit alpha 2
  • NAD(P) transhydrogenase subunit beta
KeywordsMEMBRANE PROTEIN / Membrane domain dimer
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 / SAD / Resolution: 2.77 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
DepositionDec 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9576
Polymers76,5564
Non-polymers4012
Water1629
1
A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4783
Polymers38,2782
Non-polymers2011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-114 kcal/mol
Surface area14800 Å2
MethodPISA
2
C: NAD(P) transhydrogenase subunit alpha 2
D: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4783
Polymers38,2782
Non-polymers2011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-114 kcal/mol
Surface area14890 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17440 Å2
ΔGint-257 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.408, 86.920, 98.978
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 10168.106 Da / Num. of mol.: 2
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: 28109.693 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 298 K / Method: lipidic subic phase / pH: 8.5
Details: 100 mM Tris pH 8.5, 350 mM NH4-formate, 100mM Na-thiocynate, and 18% (v/v) 1-4-butanediol, lipidic subic phase, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9993 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: 0.9993 Å / Relative weight: 1
ReflectionResolution: 2.77→98.7 Å / Num. obs: 24865 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.77→98.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.749 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.663 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26858 1354 5.2 %RANDOM
Rwork0.20406 ---
obs0.20713 24865 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.705 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.58 Å2
2--0.28 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.77→98.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 2 9 5212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195316
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9637234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37322.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.64615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5371515
X-RAY DIFFRACTIONr_chiral_restr0.1250.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213813
X-RAY DIFFRACTIONr_mcbond_it6.2278.1782828
X-RAY DIFFRACTIONr_mcangle_it8.73912.2143528
X-RAY DIFFRACTIONr_scbond_it7.6888.5922488
X-RAY DIFFRACTIONr_long_range_B_refined12.29771.5559049
LS refinement shellResolution: 2.77→2.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 62 -
Rwork0.332 1253 -
obs--65.36 %

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