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- PDB-4j16: Crystal structure of Thermus thermophilus transhydrogenase hetero... -

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Basic information

Entry
Database: PDB / ID: 4j16
TitleCrystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit
Components
  • NAD(P) transhydrogenase subunit beta
  • NAD/NADP transhydrogenase alpha subunit 1
KeywordsOXIDOREDUCTASE / Soluble components of nicotinamide nucleotide transhydrogenase / Complex of Alpha1 subunit dimer with Domain III of Beta subunit / Alpha1 binds NAD(H) / Domain III binds NADP(H) / Domain III binds to Alpha1 / NAD bound to Alpha1 / NADP bound to Domain III
Function / homology
Function and homology information


: / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / plasma membrane
Similarity search - Function
NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / 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 ...NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIETHYLENE GLYCOL / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsYamaguchi, M. / Leung, J. / Schurig Briccio, L.A. / Gennis, R.B. / Stout, C.D.
CitationJournal: To be Published
Title: Crystal structure analysis of Thermus thermophilus transhydrogenase soluble domains
Authors: Yamaguchi, M. / Leung, J. / Schurig Briccio, L.A. / Gennis, R.B. / Stout, C.D.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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/NADP transhydrogenase alpha subunit 1
B: NAD/NADP transhydrogenase alpha subunit 1
C: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,16110
Polymers101,7213
Non-polymers2,4407
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-65 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.616, 75.038, 198.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein NAD/NADP transhydrogenase alpha subunit 1


Mass: 40851.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1780 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AcrAB- / References: UniProt: Q72GR8, EC: 1.6.1.2
#2: Protein NAD(P) transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta


Mass: 20018.150 Da / Num. of mol.: 1 / Fragment: Domain III (UNP residues 266-450)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AcrAB- / References: UniProt: Q72GS0, EC: 1.6.1.2

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Non-polymers , 6 types, 128 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions MD1-47 Morpheus kit, condition E2: 0.12 M ethylene glycols, 0.1 M pH 6.5 buffers, 30% ethylene glycol + PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.18076 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2.4→39.98 Å / Num. all: 38049 / Num. obs: 36638 / % possible obs: 96.29 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4538 / Rsym value: 0.557 / % possible all: 79.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4IZH, 1PNO

4izh

1pno


Resolution: 2.41→39.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.836 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.474 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25328 1924 5 %RANDOM
Rwork0.20062 ---
all0.20331 38049 --
obs0.20331 36638 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.41→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 159 121 7186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197186
X-RAY DIFFRACTIONr_bond_other_d0.0010.027134
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.97612558
X-RAY DIFFRACTIONr_angle_other_deg0.771317250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3917.51828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91923.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.609151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7651557
X-RAY DIFFRACTIONr_chiral_restr0.0710.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022289
LS refinement shellResolution: 2.41→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 121 -
Rwork0.3 2059 -
obs-2059 75.62 %
Refinement TLS params.

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)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1384-0.60290.16122.03710.1581.0630.26970.18770.4855-0.0157-0.19120.0385-0.0616-0.0912-0.07860.04940.03260.11820.040.0790.410719.14910.001-22.677
22.4849-0.8777-0.44151.45010.41171.34320.3030.5157-0.2381-0.139-0.18930.03870.4642-0.0682-0.11370.26960.086-0.08630.1495-0.03560.230635.184-22.29-36.002
32.1053-0.0524-0.62753.0798-0.58392.3363-0.0647-0.04430.01670.111-0.01190.13250.1244-0.1050.07660.0358-0.01410.07670.0179-0.00930.266210.949-8.061.86
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 372
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B1 - 373
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C274 - 450
6X-RAY DIFFRACTION3C501

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