- PDB-4o9t: Mechanism of transhydrogenase coupling proton translocation and h... -
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Basic information
Entry
Database: PDB / ID: 4o9t
Title
Mechanism of transhydrogenase coupling proton translocation and hydride transfer
Components
NAD(P) transhydrogenase subunit alpha 2
NAD(P) transhydrogenase subunit beta
Keywords
MEMBRANE PROTEIN / Nicotinamide nucleotide transhydrogenase couples the proton motive force to NADPH formation / Integral membrane component of Thermus thermophilus transhydrogenase / Respiratory enzyme / Protons and NAD(H) / NADP(H) / Proton translocation and hydride transfer / Periplasmic membrane and cytosol
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.079→46.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.885 / SU B: 20.71 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27963
1899
5 %
RANDOM
Rwork
0.21945
-
-
-
obs
0.22249
36118
98.46 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 74.675 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.92 Å2
0 Å2
-0.32 Å2
2-
-
-1.87 Å2
-0 Å2
3-
-
-
-3.96 Å2
Refinement step
Cycle: LAST / Resolution: 3.079→46.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10352
0
0
0
10352
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.019
10570
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
10750
X-RAY DIFFRACTION
r_angle_refined_deg
1.548
1.963
14386
X-RAY DIFFRACTION
r_angle_other_deg
0.9
3
24484
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.301
5
1400
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.667
22.55
298
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
22.212
15
1650
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.798
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.084
0.2
1760
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
11766
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2392
X-RAY DIFFRACTION
r_mcbond_it
4.736
7.188
5624
X-RAY DIFFRACTION
r_mcbond_other
4.729
7.187
5623
X-RAY DIFFRACTION
r_mcangle_it
7.475
10.764
7016
X-RAY DIFFRACTION
r_mcangle_other
7.475
10.765
7017
X-RAY DIFFRACTION
r_scbond_it
4.798
7.809
4946
X-RAY DIFFRACTION
r_scbond_other
4.798
7.81
4947
X-RAY DIFFRACTION
r_scangle_other
7.462
11.515
7371
X-RAY DIFFRACTION
r_long_range_B_refined
10.617
59.946
12935
X-RAY DIFFRACTION
r_long_range_B_other
10.616
59.95
12936
LS refinement shell
Resolution: 3.079→3.158 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.373
118
-
Rwork
0.322
2639
-
obs
-
-
98.36 %
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