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- PDB-1ptj: Crystal structure analysis of the DI and DIII complex of transhyd... -

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Basic information

Entry
Database: PDB / ID: 1ptj
TitleCrystal structure analysis of the DI and DIII complex of transhydrogenase with a thio-nicotinamide nucleotide analogue
Components(NAD(P) transhydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Transhydrogenase / thio-nicotinamide / mitochondria / proton translocation
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 / membrane => GO:0016020 / NAD binding / NADP binding / 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 / THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P) transhydrogenase subunit alpha part 1 / NAD(P) transhydrogenase subunit beta / 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: 2.61 Å
AuthorsSingh, A. / Venning, J.D. / Quirk, P.G. / van Boxel, G.I. / Rodrigues, D.J. / White, S.A. / Jackson, J.B.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Interactions between transhydrogenase and thio-nicotinamide analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation
Authors: Singh, A. / Venning, J.D. / Quirk, P.G. / Van Boxel, G.I. / Rodrigues, D.J. / White, S.A. / Jackson, J.B.
History
DepositionJun 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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)100,5868
Polymers98,8873
Non-polymers1,6995
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-45 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.089, 74.698, 205.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / 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: 40068.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria)
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 NADP(H)-binding component / dIII


Mass: 18749.463 Da / Num. of mol.: 1 / Fragment: residues 291-464 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria)
References: UniProt: Q59765, UniProt: Q2RSB4*PLUS, EC: 1.6.1.2

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-SND / THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 679.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O13P2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 146 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 100K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Cotton, N.P., (2001) Structure, 9, 165.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES1reservoir
214-17 %PEG80001reservoir
3100-200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.61→42.26 Å / Num. all: 164967 / Num. obs: 162328 / % possible obs: 98.4 % / Biso Wilson estimate: 76.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 6.1
Reflection shellResolution: 2.61→2.75 Å / Mean I/σ(I) obs: 2 / Num. unique all: 4856 / Rsym value: 0.339 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 33781 / Redundancy: 4.8 % / Num. measured all: 162328 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 98.4 % / Redundancy: 4.8 % / Num. unique obs: 4856 / Num. measured obs: 23435 / Rmerge(I) obs: 0.339

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZZ

1hzz


Resolution: 2.61→42.26 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 --RANDOM
Rwork0.234 ---
all-164967 --
obs-162328 98.4 %-
Displacement parametersBiso mean: 67.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.047 Å20 Å20 Å2
2---9.292 Å20 Å2
3---16.339 Å2
Refinement stepCycle: LAST / Resolution: 2.61→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 110 146 6924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0075
X-RAY DIFFRACTIONc_angle_d1.387
LS refinement shellResolution: 2.61→2.65 Å
RfactorNum. reflection% reflection
Rfree0.287 --
Rwork0.235 --
obs-162238 98.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2thio_nuc2.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4glycerol.par
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.2871 / Rfactor Rwork: 0.2352
Solvent computation
*PLUS
Displacement parameters
*PLUS

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