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- PDB-1x14: Crystal structure of E. coli transhydrogenase domain I with bound NAD -

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Basic information

Entry
Database: PDB / ID: 1x14
TitleCrystal structure of E. coli transhydrogenase domain I with bound NAD
ComponentsNAD(P) transhydrogenase subunit alpha
KeywordsOXIDOREDUCTASE / Transhydrogenase / NAD(H)-binding domain / Rossmann fold
Function / homology
Function and homology information


proton export across plasma membrane / : / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / protein dimerization activity / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / 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 ...NAD(P) transhydrogenase, alpha subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P) transhydrogenase subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJohansson, T. / Oswald, C. / Pedersen, A. / Tornroth, S. / Okvist, M. / Karlsson, B.G. / Rydstrom, J. / Krengel, U.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: X-ray Structure of Domain I of the Proton-pumping Membrane Protein Transhydrogenase from Escherichia coli
Authors: Johansson, T. / Oswald, C. / Pedersen, A. / Tornroth, S. / Okvist, M. / Karlsson, B.G. / Rydstrom, J. / Krengel, U.
History
DepositionMar 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: NAD(P) transhydrogenase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3913
Polymers85,7282
Non-polymers6631
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-17 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.773, 66.985, 76.619
Angle α, β, γ (deg.)67.08, 80.69, 80.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NAD(P) transhydrogenase subunit alpha / Pyridine nucleotide transhydrogenase subunit alpha / Nicotinamide nucleotide transhydrogenase subunit alpha


Mass: 42863.883 Da / Num. of mol.: 2 / Fragment: NAD(H)-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5alpha / Gene: pntA / Plasmid: pDC21 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P07001, EC: 1.6.1.2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium acetate, trisodium citrate dihydrate, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 / Date: Nov 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 48479 / Num. obs: 46043 / % possible obs: 94.1 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7
Reflection shellResolution: 1.94→2.01 Å / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.057 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.7 / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25763 2434 5 %RANDOM
Rwork0.20388 ---
all0.20659 48479 --
obs0.20659 46043 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.472 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å2-2.14 Å23.3 Å2
2---0.92 Å2-0.86 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 44 167 5673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225598
X-RAY DIFFRACTIONr_bond_other_d0.0020.025261
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9747613
X-RAY DIFFRACTIONr_angle_other_deg0.888312228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0625726
X-RAY DIFFRACTIONr_chiral_restr0.0960.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026217
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021030
X-RAY DIFFRACTIONr_nbd_refined0.2160.21074
X-RAY DIFFRACTIONr_nbd_other0.2390.26005
X-RAY DIFFRACTIONr_nbtor_other0.0860.23307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.27
X-RAY DIFFRACTIONr_mcbond_it0.9471.53623
X-RAY DIFFRACTIONr_mcangle_it1.65625836
X-RAY DIFFRACTIONr_scbond_it2.40131975
X-RAY DIFFRACTIONr_scangle_it3.9144.51777
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 151
Rwork0.305 3034

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