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- PDB-1djl: THE CRYSTAL STRUCTURE OF HUMAN TRANSHYDROGENASE DOMAIN III WITH B... -

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Basic information

Entry
Database: PDB / ID: 1djl
TitleTHE CRYSTAL STRUCTURE OF HUMAN TRANSHYDROGENASE DOMAIN III WITH BOUND NADP
ComponentsTRANSHYDROGENASE DIII
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD DINUCLEOTIDE BINDING FOLD REVERSE BINDING OF NADP
Function / homology
Function and homology information


response to vitamin / NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / Citric acid cycle (TCA cycle) / NADPH regeneration / intracellular oxygen homeostasis / : / positive regulation of hydrogen peroxide catabolic process / positive regulation of mitochondrial membrane potential ...response to vitamin / NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / Citric acid cycle (TCA cycle) / NADPH regeneration / intracellular oxygen homeostasis / : / positive regulation of hydrogen peroxide catabolic process / positive regulation of mitochondrial membrane potential / cellular oxidant detoxification / tricarboxylic acid cycle / cell redox homeostasis / proton transmembrane transport / reactive oxygen species metabolic process / negative regulation of protein phosphorylation / NAD binding / NADP binding / mitochondrial inner membrane / negative regulation of apoptotic process / mitochondrion / membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / 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 ...NAD(P) transhydrogenase, alpha subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / 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 domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P) transhydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWhite, S.A. / Peak, S.J. / Cotton, N.P. / Jackson, J.B.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The high-resolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from human heart mitochondria.
Authors: White, S.A. / Peake, S.J. / McSweeney, S. / Leonard, G. / Cotton, N.P. / Jackson, J.B.
#1: Journal: To be Published
Title: Structure and Mechanism of Proton-Translocating Transhydrogenase: A Mini-Review
Authors: Jackson, J.B. / Peak, S.J. / White, S.A.
#2: Journal: To be Published
Title: The NADPH-Binding Component (dIII) of Human-Heart Transhydrogenase: Crystallisation and Preliminary Crystallographic Analysis
Authors: Peak, S.J. / Jackson, J.B. / White, S.A.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: TRANSHYDROGENASE DIII
B: TRANSHYDROGENASE DIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4268
Polymers44,5632
Non-polymers1,8636
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.104, 58.104, 250.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein TRANSHYDROGENASE DIII


Mass: 22281.652 Da / Num. of mol.: 2 / Fragment: RESIDUES 837-1086
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: Q13423, EC: 1.6.1.1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AMMONIUM SULPHATE, MOPS, DIOXANE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: SJ Peake, JB Jackeson and SA White, unpublished data

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementHighest resolution: 2 Å /
RfactorNum. reflection
Rfree0.2582 -
obs0.2373 35132
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 118 80 2952
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.42

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