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- PDB-1pt9: Crystal Structure Analysis of the DIII Component of Transhydrogen... -

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Basic information

Entry
Database: PDB / ID: 1pt9
TitleCrystal Structure Analysis of the DIII Component of Transhydrogenase with a Thio-Nicotinamide Nucleotide Analogue
ComponentsNAD(P) transhydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / Transhydrogenase / thio-nicotinamide / mitochondria / proton translocation
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
7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P) transhydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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, mitochondrial
B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4598
Polymers44,5632
Non-polymers1,8956
Water3,081171
1
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2294
Polymers22,2821
Non-polymers9483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2294
Polymers22,2821
Non-polymers9483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules

A: NAD(P) transhydrogenase, mitochondrial
hetero molecules

B: NAD(P) transhydrogenase, mitochondrial
hetero molecules

B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,91716
Polymers89,1274
Non-polymers3,79112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation8_655-y+1,-x,-z+1/41
Buried area12020 Å2
ΔGint-91 kcal/mol
Surface area29840 Å2
MethodPISA
4
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules

B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4598
Polymers44,5632
Non-polymers1,8956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5450 Å2
ΔGint-38 kcal/mol
Surface area15480 Å2
MethodPISA
5
A: NAD(P) transhydrogenase, mitochondrial
hetero molecules

A: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4598
Polymers44,5632
Non-polymers1,8956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area4370 Å2
ΔGint-41 kcal/mol
Surface area16500 Å2
MethodPISA
6
B: NAD(P) transhydrogenase, mitochondrial
hetero molecules

B: NAD(P) transhydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4598
Polymers44,5632
Non-polymers1,8956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4690 Å2
ΔGint-39 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.400, 57.400, 251.130
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-322-

HOH

21B-368-

HOH

31B-377-

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 / Fragment: residues 880-1086 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Heart / 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-TAP / 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TATP


Mass: 759.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O16P3S
#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.: 171 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: unpublished data, White, S.A., (2000) Structure Fold.Des., 8, 1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.42→36.82 Å / Num. all: 102352 / Num. obs: 100817 / % possible obs: 98.5 % / Biso Wilson estimate: 50.91 Å2 / Rsym value: 0.077 / Net I/σ(I): 6.8
Reflection shellResolution: 2.42→2.55 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 2312 / Rsym value: 0.319 / % possible all: 96.2
Reflection
*PLUS
Num. obs: 16825 / Redundancy: 6 % / Num. measured all: 100817 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 96.2 % / Redundancy: 4.9 % / Num. unique obs: 2312 / Num. measured obs: 11365 / Rmerge(I) obs: 0.319

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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: PDB ENTRY 1DJL

1djl


Resolution: 2.42→36.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 --RANDOM
Rwork0.219 ---
all-102352 --
obs-100817 98.5 %-
Displacement parametersBiso mean: 38.71 Å2
Refinement stepCycle: LAST / Resolution: 2.42→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 118 171 3043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_angle_d1.247
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_scbond_it1.9822
X-RAY DIFFRACTIONc_mcangle_it2.3412
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.42→2.45 Å
RfactorNum. reflection% reflection
Rfree0.278 5040 -
Rwork0.219 --
obs-100817 98.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2thio_het.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
Refinement
*PLUS
Lowest resolution: 36.82 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.2187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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