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- PDB-1u31: recombinant human heart transhydrogenase dIII bound with NADPH -

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Basic information

Entry
Database: PDB / ID: 1u31
Titlerecombinant human heart transhydrogenase dIII bound with NADPH
ComponentsNAD(P) transhydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / NAD(P) transhydrogenase / 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) / intracellular oxygen homeostasis / NADPH regeneration / respiratory chain complex / 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) / intracellular oxygen homeostasis / NADPH regeneration / respiratory chain complex / positive regulation of hydrogen peroxide catabolic process / positive regulation of mitochondrial membrane potential / cellular oxidant detoxification / tricarboxylic acid cycle / proton transmembrane transport / reactive oxygen species metabolic process / cell redox homeostasis / 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/pyridine nucleotide transhydrogenase, N-terminal ...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/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 domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / NAD(P) transhydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMather, O.C. / Singh, A. / van Boxel, G.I. / White, S.A. / Jackson, J.B.
CitationJournal: Biochemistry / Year: 2004
Title: Active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase.
Authors: Mather, O.C. / Singh, A. / van Boxel, G.I. / White, S.A. / Jackson, J.B.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2013Group: Non-polymer description
Revision 1.4Aug 23, 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, mitochondrial
B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4308
Polymers44,5632
Non-polymers1,8676
Water3,927218
1
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2154
Polymers22,2821
Non-polymers9343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2154
Polymers22,2821
Non-polymers9343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules

B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4308
Polymers44,5632
Non-polymers1,8676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5370 Å2
ΔGint-33 kcal/mol
Surface area15640 Å2
MethodPISA
4
B: NAD(P) transhydrogenase, mitochondrial
hetero molecules

B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4308
Polymers44,5632
Non-polymers1,8676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4800 Å2
ΔGint-45 kcal/mol
Surface area16640 Å2
MethodPISA
5
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules

A: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4308
Polymers44,5632
Non-polymers1,8676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area4020 Å2
ΔGint-20 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.814, 57.814, 250.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-526-

HOH

31B-540-

HOH

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Components

#1: Protein NAD(P) transhydrogenase, mitochondrial / Pyridine nucleotide transhydrogenase / Nicotinamide nucleotide transhydrogenase


Mass: 22281.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNT / Production host: Escherichia coli (E. coli) / References: UniProt: Q13423, EC: 1.6.1.2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#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.: 218 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, MES, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→63 Å / Num. obs: 19463 / % possible obs: 82.4 % / Redundancy: 3.2 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1djl

1djl


Resolution: 2.2→31.7 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.817 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26841 947 5.1 %RANDOM
Rwork0.22956 ---
obs0.23164 17612 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.057 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 118 218 3090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222924
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9662.0273988
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9895362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38226.071112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35215490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6991510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.21467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21995
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3211.51891
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57422938
X-RAY DIFFRACTIONr_scbond_it0.33731177
X-RAY DIFFRACTIONr_scangle_it0.5624.51050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 23 -
Rwork0.263 508 -
obs--100 %
Refinement TLS params.

T12: 0.0133 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6224-0.1572-0.09750.99410.06060.984-0.01150.01720.0447-0.04190.01990.0071-0.0428-0.0964-0.0085-0.01620.0032-0.01180.019-0.034437.638633.976216.1564
20.9039-0.25590.29710.7478-0.06270.65040.02280.006-0.07530.0159-0.0093-0.01050.03980.0745-0.0135-0.0291-0.0102-0.0050.0021-0.03275.082913.984615.1932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA - E23 - 30023 - 1
2X-RAY DIFFRACTION2BB - F23 - 40023 - 1

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