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- PDB-2fr8: Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymm... -

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Basic information

Entry
Database: PDB / ID: 2fr8
TitleStructure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex
Components
  • NAD(P) transhydrogenase subunit alpha part 1
  • NAD(P) transhydrogenase subunit beta
KeywordsOXIDOREDUCTASE / NAD(P) TRANSHYDROGENASE SUBUNITS / NAD+ / NADP+
Function / homology
Function and homology information


NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADH binding / NAD+ binding / NAD binding / NADP binding / membrane => GO:0016020 / protein dimerization activity / plasma membrane
Similarity search - Function
NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit alpha part 1 / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit alpha part 1
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrondijk, T.H. / van Boxel, G.I. / Mather, O.C. / Quirk, P.G. / White, S.A. / Jackson, J.B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Role of Invariant Amino Acid Residues at the Hydride Transfer Site of Proton-translocating Transhydrogenase.
Authors: Brondijk, T.H. / van Boxel, G.I. / Mather, O.C. / Quirk, P.G. / White, S.A. / Jackson, J.B.
History
DepositionJan 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600LIGAND NAD 500 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN A. NAP 400 IS ASSOCIATED WITH ...LIGAND NAD 500 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN A. NAP 400 IS ASSOCIATED WITH TRANSHYDROGENASE DIII CHAIN C.

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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 part 1
B: NAD(P) transhydrogenase subunit alpha part 1
C: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3705
Polymers101,9633
Non-polymers1,4072
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-42 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.130, 70.330, 195.140
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 NAD(P) transhydrogenase subunit alpha part 1 / Pyridine nucleotide transhydrogenase subunit alpha 1 / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit alpha 1 / Nicotinamide nucleotide transhydrogenase subunit alpha 1 / Proton-translocating transhydrogenase component 1 / dI


Mass: 40238.672 Da / Num. of mol.: 2 / Mutation: R127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntAA, nntA1 / Plasmid: pGVB3 / Production host: Escherichia coli (E. coli) / Strain (production host): C600
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.2
#2: Protein NAD(P) transhydrogenase subunit beta / Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta / Proton-translocating transhydrogenase NADPH / -binding component / dIII


Mass: 21485.510 Da / Num. of mol.: 1 / Fragment: dIII domain transhydrogenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntB, nntB / Plasmid: pNIC2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q59765, UniProt: P0C188*PLUS, EC: 1.6.1.2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 16-20% 8K-PEG, 20-150 mM (NH4)2SO4, 100 mM Mes, pH 6.0 and 10% glycerol in the presence of 50 mM NAD+ and 5 mM NADP+, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→47.7 Å / Num. all: 27222 / Num. obs: 27222 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 41.29 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 11.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3653 / Rsym value: 0.442 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HZZ

1hzz


Resolution: 2.6→41.3 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.855 / SU B: 33.928 / SU ML: 0.345 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30388 1381 5.1 %RANDOM
Rwork0.25059 ---
all0.25328 25781 --
obs0.25328 25781 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.122 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2---1.53 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 75 56 6599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226640
X-RAY DIFFRACTIONr_bond_other_d0.0060.026378
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9989021
X-RAY DIFFRACTIONr_angle_other_deg0.849314834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.77324.932219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.449151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4771532
X-RAY DIFFRACTIONr_chiral_restr0.0580.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027260
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021145
X-RAY DIFFRACTIONr_nbd_refined0.180.31542
X-RAY DIFFRACTIONr_nbd_other0.1770.36907
X-RAY DIFFRACTIONr_nbtor_refined0.1610.53248
X-RAY DIFFRACTIONr_nbtor_other0.0830.53614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5315
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0610.58
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.397
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.58
X-RAY DIFFRACTIONr_mcbond_it0.3941.54489
X-RAY DIFFRACTIONr_mcbond_other0.0251.51787
X-RAY DIFFRACTIONr_mcangle_it0.68127044
X-RAY DIFFRACTIONr_scbond_it0.33832363
X-RAY DIFFRACTIONr_scangle_it0.564.51977
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 89 -
Rwork0.356 1699 -
obs--89.49 %
Refinement TLS params.Method: refined / Origin x: 2.826 Å / Origin y: 68.145 Å / Origin z: 24.21 Å
111213212223313233
T-0.0829 Å20.0159 Å20.0291 Å2--0.0701 Å2-0.005 Å2--0.0584 Å2
L0.1275 °20.188 °20.0554 °2-0.3639 °20.0878 °2--0.2164 °2
S0.0103 Å °0.0106 Å °0.032 Å °0.0322 Å °-0.0045 Å °0.0568 Å °-0.0025 Å °-0.0044 Å °-0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3711 - 371
2X-RAY DIFFRACTION1BB1 - 3751 - 375
3X-RAY DIFFRACTION1CC30 - 20330 - 203

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