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- PDB-1d4o: CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1d4o
TitleCRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS RESOLUTION
ComponentsNADP(H) TRANSHYDROGENASE
KeywordsOXIDOREDUCTASE / NUCLEOTIDE-BINDING FOLD / PROTEIN-NADP(H) COMPLEX / INVERTED BINDING OF NADP(H)
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / reactive oxygen species metabolic process / NADP binding / oxidoreductase activity / mitochondrial inner 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P) transhydrogenase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.21 Å
AuthorsPrasad, G.S. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of transhydrogenase domain III at 1.2 A resolution.
Authors: Prasad, G.S. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D.
History
DepositionOct 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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: NADP(H) TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7612
Polymers20,0181
Non-polymers7431
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.66, 36.73, 38.49
Angle α, β, γ (deg.)68.36, 87.99, 74.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NADP(H) TRANSHYDROGENASE


Mass: 20018.066 Da / Num. of mol.: 1 / Fragment: NADP(H) BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIA / Production host: Escherichia coli (E. coli)
References: UniProt: P11024, NAD(P)+ transhydrogenase (Si-specific)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 24% w/v MPEG 5000, 100mM sodium cacodylate and 200mM magnesium acetate., pH 7.4, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl1drop
21 mMEDTA1drop
31 mMdithiothreitol1drop
40.5 mMPMSF1drop
510 mg/mlprotain1drop
624 %(w/v)mPEG50001reservoir
7100 mMsodium cacodylate1reservoir
8200 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.21→54.1 Å / Num. all: 89452 / Num. obs: 45717 / % possible obs: 91.2 % / Observed criterion σ(I): 2.3 / Redundancy: 2 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 4
Reflection shellResolution: 1.21→1.24 Å / Redundancy: 91.2 % / Rmerge(I) obs: 0.301 / Num. unique all: 2682 / % possible all: 72.3
Reflection
*PLUS
Num. measured all: 89452
Reflection shell
*PLUS
% possible obs: 72.3 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.21→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Shelx least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1383 -Random
Rwork0.168 ---
all0.167 45717 --
obs0.167 44334 91.2 %-
Refinement stepCycle: LAST / Resolution: 1.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 48 185 1576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d1.7
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 1.7

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