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- PDB-4j1t: Crystal structure of Thermus thermophilus transhydrogenase hetero... -

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Basic information

Entry
Database: PDB / ID: 4j1t
TitleCrystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit in P2(1)
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 / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 2, 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
D: NAD/NADP transhydrogenase alpha subunit 1
E: NAD/NADP transhydrogenase alpha subunit 1
F: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,62414
Polymers203,4426
Non-polymers3,1828
Water4,179232
1
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)103,2206
Polymers101,7213
Non-polymers1,4993
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-47 kcal/mol
Surface area35980 Å2
MethodPISA
2
D: NAD/NADP transhydrogenase alpha subunit 1
E: NAD/NADP transhydrogenase alpha subunit 1
F: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4048
Polymers101,7213
Non-polymers1,6835
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-47 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.075, 68.866, 132.335
Angle α, β, γ (deg.)90.00, 91.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABDECF

#1: Protein
NAD/NADP transhydrogenase alpha subunit 1


Mass: 40851.340 Da / Num. of mol.: 4
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.: 2 / 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 , 4 types, 240 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions MD1-47 Morpheus kit, condition H2: 0.10 M amino acids, 0.1 M pH 6.5 buffers, 30.0% 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: 2.37→132.35 Å / Num. all: 79373 / Num. obs: 75579 / % possible obs: 95.22 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 2.37→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10491 / Rsym value: 0.366 / % possible all: 92

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J16

4j16


Resolution: 2.37→132.35 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.702 / SU ML: 0.145 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25298 4019 5 %RANDOM
Rwork0.2047 ---
all0.20719 79373 --
obs0.20719 75579 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-2.38 Å2
2--2.66 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.37→132.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13813 0 208 232 14253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02116089
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.96924958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5527.53654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52423.586541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.868152440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.90515113
X-RAY DIFFRACTIONr_chiral_restr0.1070.22268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118265
X-RAY DIFFRACTIONr_mcbond_it0.6241.59124
X-RAY DIFFRACTIONr_mcangle_it1.189214622
X-RAY DIFFRACTIONr_scbond_it2.02135138
X-RAY DIFFRACTIONr_scangle_it3.434.54743
LS refinement shellResolution: 2.37→2.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 119 -
Rwork0.239 2319 -
obs-2319 39.95 %
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)
10.21570.0676-0.01220.64650.25890.55410.00010.00460.0272-0.02110.0010.02160.00650.0528-0.00110.1232-0.00210.15890.0064-0.0110.212-44.06116.3-31.428
20.4979-0.3699-0.1811.03630.2620.4902-0.0221-0.0320.0596-0.06670.0514-0.08330.02610.1334-0.02930.12720.01780.15630.0620.00010.1827-20.715-0.116-56.86
31.5897-0.38360.50110.72950.14161.83370.07830.0470.0809-0.03160.0461-0.0365-0.091-0.181-0.12440.1160.03850.15060.05450.02790.1774-61.52223.428-56.888
40.5140.38080.16910.74320.14970.3556-0.01360.0739-0.05240.08240.0551-0.04810.01760.0349-0.04150.16170.00850.1830.00230.00740.2434-77.401-5.363-7.999
50.43870.32220.19331.17820.77520.8724-0.06580.12350.0315-0.13630.04680.0927-0.0594-0.04590.0190.1702-0.02710.1460.04490.01460.1929-101.26-21.258-33.957
61.7153-0.16510.05880.65240.49271.3386-0.1137-0.13990.0292-0.02220.0426-0.0149-0.1275-0.10040.07110.13120.04180.15010.01980.00430.1983-104.2642.9826.305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 373
2X-RAY DIFFRACTION2B-2 - 373
3X-RAY DIFFRACTION2B500
4X-RAY DIFFRACTION3C274 - 450
5X-RAY DIFFRACTION3C500
6X-RAY DIFFRACTION4D1 - 372
7X-RAY DIFFRACTION5E1 - 373
8X-RAY DIFFRACTION5E500
9X-RAY DIFFRACTION6F274 - 450
10X-RAY DIFFRACTION6F500

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