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- PDB-2oo5: Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetri... -

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Basic information

Entry
Database: PDB / ID: 2oo5
TitleStructure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)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 / NADPH regeneration / NADH binding / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-TXD / 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
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 25, 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: Version format compliance
Revision 1.3Aug 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)101,86210
Polymers99,3993
Non-polymers2,4637
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-116 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.199, 101.025, 131.721
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, 34 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TXD / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 667.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N7O14P2
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 18% PEG 4000, 10% glycerol, 100mM Tris, 75mM lithium sulphate, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.6→80.163 Å / Num. obs: 27548 / % possible obs: 92.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.743.10.2273.31251240460.22794.4
2.74-2.913.80.17841463238030.17894.2
2.91-3.113.90.1265.71392035870.12693.8
3.11-3.363.90.097.71287433130.0993
3.36-3.683.90.079.21181030350.0792.9
3.68-4.113.90.06110.21082427610.06192.3
4.11-4.753.90.05510.3955424510.05591.7
4.75-5.813.90.0559.6796320320.05590.8
5.81-8.223.90.05210618315990.05289.7
8.22-62.623.50.051032539210.0588.8

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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: PDB ENTRY 1U2D

1u2d


Resolution: 2.6→80.06 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.859 / SU B: 21.556 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1396 5.1 %RANDOM
Rwork0.219 ---
obs0.222 27507 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.228 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.91 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.6→80.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6899 0 156 27 7082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227162
X-RAY DIFFRACTIONr_bond_other_d0.0020.026792
X-RAY DIFFRACTIONr_angle_refined_deg1.2522.0099733
X-RAY DIFFRACTIONr_angle_other_deg0.934315809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6065931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14724.876242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.661151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0411536
X-RAY DIFFRACTIONr_chiral_restr0.0640.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021251
X-RAY DIFFRACTIONr_nbd_refined0.1420.31325
X-RAY DIFFRACTIONr_nbd_other0.1240.36628
X-RAY DIFFRACTIONr_nbtor_refined0.1470.53411
X-RAY DIFFRACTIONr_nbtor_other0.0790.53818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.5240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0630.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1080.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.53
X-RAY DIFFRACTIONr_mcbond_it0.97426015
X-RAY DIFFRACTIONr_mcbond_other0.13521902
X-RAY DIFFRACTIONr_mcangle_it1.14937475
X-RAY DIFFRACTIONr_scbond_it0.61922820
X-RAY DIFFRACTIONr_scangle_it0.9732258
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 108 -
Rwork0.308 1928 -
obs-2036 93.78 %
Refinement TLS params.Method: refined / Origin x: 48.9347 Å / Origin y: 55.9314 Å / Origin z: 119.4688 Å
111213212223313233
T-0.0944 Å2-0.002 Å2-0.017 Å2--0.1236 Å2-0.0024 Å2---0.083 Å2
L0.951 °2-0.021 °20.3322 °2-0.643 °2-0.0601 °2--0.5113 °2
S0.1265 Å °-0.0242 Å °-0.0132 Å °-0.0909 Å °-0.04 Å °-0.0081 Å °0.0378 Å °0.054 Å °-0.0866 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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