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- PDB-2oor: Structure of transhydrogenase (dI.NAD+)2(dIII.H2NADPH)1 asymmetri... -

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Basic information

Entry
Database: PDB / ID: 2oor
TitleStructure of transhydrogenase (dI.NAD+)2(dIII.H2NADPH)1 asymmetric complex
Components(NAD(P) transhydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD(H)-binding site / NADP(H)-binding site
Function / homology
Function and homology information


NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADH binding / NADPH regeneration / NAD+ binding / NAD binding / NADP binding / oxidoreductase activity / 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/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / 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/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / 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 / Chem-TXP / 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: 2.32 Å
AuthorsBhakta, T. / Jackson, J.B.
CitationJournal: Biochemistry / Year: 2007
Title: Structures of the dI(2)dIII(1) Complex of Proton-Translocating Transhydrogenase with Bound, Inactive Analogues of NADH and NADPH Reveal Active Site Geometries
Authors: Bhakta, T. / Whitehead, S.J. / Snaith, J.S. / Dafforn, T.R. / Wilkie, J. / Rajesh, S. / White, S.A. / Jackson, J.B.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 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)101,5657
Polymers99,3993
Non-polymers2,1664
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-49 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.194, 74.451, 204.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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NAD(P) transhydrogenase subunit ... , 2 types, 3 molecules ABC

#1: Protein NAD(P) transhydrogenase subunit alpha part 1 / E.C.1.6.1.2 / 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: 40324.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntAA, nntA1 / Plasmid: pCD1 / Production host: Escherichia coli (E. coli) / Strain (production host): C600
References: UniProt: P0C186, UniProt: Q2RSB2*PLUS, EC: 1.6.1.2
#2: Protein NAD(P) transhydrogenase subunit beta / E.C.1.6.1.2 / Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta / Proton-translocating transhydrogenase NADP(H)-binding component / dIII


Mass: 18749.463 Da / Num. of mol.: 1 / Fragment: residues 262-464
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: P0C188, EC: 1.6.1.2

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TXP / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 747.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Mes, 16% PEG 4K, 10% glycerol, 50mM ammonium sulphate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MAR CCD 130 mm / 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: 2.32→102.629 Å / Num. obs: 44362 / % possible obs: 91.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.32-2.453.60.3172.31703847260.31769
2.45-2.594.10.2332.92328157450.23386.8
2.59-2.774.10.1644.22322856330.16490.6
2.77-34.10.115.82250655120.1194.8
3-3.284.10.0738.22139752420.07397.5
3.28-3.674.20.04912.32047448420.04999.3
3.67-4.244.40.04113.61892443400.04199.7
4.24-5.194.60.0412.81696837190.0499.8
5.19-7.344.60.0413.51341029160.0499.8
7.34-68.044.10.03813.5699916870.03899

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U2D

1u2d


Resolution: 2.32→102.6 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / SU B: 15.88 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2530 5.7 %RANDOM
Rwork0.247 ---
obs0.249 44314 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.352 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---0.25 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.32→102.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 134 91 6981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226997
X-RAY DIFFRACTIONr_bond_other_d0.0020.026669
X-RAY DIFFRACTIONr_angle_refined_deg1.3372.0069504
X-RAY DIFFRACTIONr_angle_other_deg0.982315522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46124.788236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.832151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1541536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021220
X-RAY DIFFRACTIONr_nbd_refined0.140.31266
X-RAY DIFFRACTIONr_nbd_other0.1290.36537
X-RAY DIFFRACTIONr_nbtor_refined0.1460.53307
X-RAY DIFFRACTIONr_nbtor_other0.0790.53720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5324
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0550.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1020.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.55
X-RAY DIFFRACTIONr_mcbond_it1.12725876
X-RAY DIFFRACTIONr_mcbond_other0.15221863
X-RAY DIFFRACTIONr_mcangle_it1.32637322
X-RAY DIFFRACTIONr_scbond_it0.70522716
X-RAY DIFFRACTIONr_scangle_it1.09132182
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 128 -
Rwork0.295 2055 -
obs-2183 62.07 %
Refinement TLS params.Method: refined / Origin x: -15.4552 Å / Origin y: -19.2289 Å / Origin z: 23.594 Å
111213212223313233
T-0.1292 Å20.0701 Å2-0.0218 Å2--0.1017 Å2-0.0344 Å2---0.213 Å2
L2.0127 °20.6683 °2-0.4505 °2-0.6291 °2-0.1561 °2--0.8324 °2
S-0.0179 Å °0.2393 Å °0.0294 Å °0.0549 Å °0.1074 Å °0.0297 Å °-0.0792 Å °0.0028 Å °-0.0895 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA1 - 2691 - 269
2BB1 - 2801 - 280
3CC30 - 2021 - 173

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