- PDB-7ya4: Formate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7ya4
Title
Formate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide
Components
Formate dehydrogenase
Keywords
OXIDOREDUCTASE / Formate dehydrogenase / Complex / NAD
Function / homology
Function and homology information
formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytoplasm Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily Similarity search - Domain/homology
Resolution: 1.8→34.138 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.5 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.109 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1908
7007
4.988 %
Rwork
0.1552
133479
-
all
0.157
-
-
obs
-
140486
97.707 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 17.076 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.855 Å2
-0 Å2
-1.96 Å2
2-
-
1.168 Å2
0 Å2
3-
-
-
-1.312 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→34.138 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11796
0
135
965
12896
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.012
12231
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
11110
X-RAY DIFFRACTION
r_angle_refined_deg
1.533
1.641
16612
X-RAY DIFFRACTION
r_angle_other_deg
0.527
1.555
25920
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.136
5
1513
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
10.777
10
72
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.134
10
1994
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
16.154
10
530
X-RAY DIFFRACTION
r_chiral_restr
0.078
0.2
1810
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
13849
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2350
X-RAY DIFFRACTION
r_nbd_refined
0.219
0.2
2341
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.183
0.2
10387
X-RAY DIFFRACTION
r_nbtor_refined
0.176
0.2
5901
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.078
0.2
6054
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.129
0.2
774
X-RAY DIFFRACTION
r_metal_ion_refined
0.069
0.2
3
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.155
0.2
19
X-RAY DIFFRACTION
r_nbd_other
0.168
0.2
63
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.115
0.2
19
X-RAY DIFFRACTION
r_mcbond_it
1.346
1.705
6065
X-RAY DIFFRACTION
r_mcbond_other
1.338
1.704
6064
X-RAY DIFFRACTION
r_mcangle_it
1.826
2.55
7573
X-RAY DIFFRACTION
r_mcangle_other
1.826
2.55
7574
X-RAY DIFFRACTION
r_scbond_it
2.247
1.949
6166
X-RAY DIFFRACTION
r_scbond_other
2.247
1.949
6167
X-RAY DIFFRACTION
r_scangle_it
3.502
2.813
9039
X-RAY DIFFRACTION
r_scangle_other
3.502
2.813
9040
X-RAY DIFFRACTION
r_lrange_it
4.207
24.85
13747
X-RAY DIFFRACTION
r_lrange_other
4.17
24.456
13540
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.8-1.847
0.243
483
0.213
9430
0.214
10541
0.953
0.966
94.0423
0.177
1.847-1.897
0.241
514
0.201
9467
0.203
10324
0.959
0.971
96.6776
0.166
1.897-1.952
0.21
471
0.185
9243
0.186
10019
0.969
0.976
96.9558
0.153
1.952-2.012
0.221
456
0.179
8981
0.181
9706
0.965
0.979
97.2285
0.151
2.012-2.077
0.206
463
0.165
8794
0.167
9462
0.973
0.982
97.8334
0.14
2.077-2.15
0.218
473
0.164
8493
0.167
9130
0.97
0.983
98.2037
0.144
2.15-2.231
0.204
444
0.152
8184
0.154
8813
0.973
0.985
97.9008
0.134
2.231-2.322
0.198
403
0.15
7860
0.152
8466
0.976
0.986
97.6022
0.131
2.322-2.424
0.192
411
0.146
7601
0.148
8173
0.978
0.987
98.0301
0.13
2.424-2.542
0.186
379
0.142
7241
0.145
7778
0.979
0.988
97.9686
0.128
2.542-2.679
0.203
346
0.145
6894
0.147
7397
0.977
0.987
97.8775
0.132
2.679-2.84
0.18
341
0.147
6585
0.149
7057
0.98
0.987
98.1437
0.138
2.84-3.035
0.196
326
0.158
6153
0.16
6584
0.977
0.985
98.4052
0.15
3.035-3.276
0.189
316
0.164
5783
0.165
6155
0.978
0.984
99.0902
0.161
3.276-3.585
0.198
271
0.163
5379
0.165
5687
0.979
0.986
99.3494
0.165
3.585-4.003
0.172
268
0.15
4862
0.151
5154
0.984
0.988
99.5343
0.155
4.003-4.611
0.144
233
0.124
4294
0.125
4554
0.989
0.992
99.4071
0.135
4.611-5.622
0.144
177
0.135
3679
0.136
3892
0.989
0.991
99.075
0.15
5.622-7.845
0.175
147
0.144
2878
0.146
3032
0.985
0.99
99.7691
0.159
7.845-34.138
0.194
85
0.147
1678
0.149
1785
0.986
0.99
98.7675
0.18
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