inositol oxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / inositol oxygenase activity / inositol catabolic process / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / aldo-keto reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H / inclusion body / ferric iron binding ...inositol oxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / inositol oxygenase activity / inositol catabolic process / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / aldo-keto reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H / inclusion body / ferric iron binding / cytoplasm / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 100 mM Tris pH 7.8, 1.8 M Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution: 1.5→30 Å / Num. obs: 140563 / % possible obs: 67.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.21
Reflection shell
Resolution: 1.5→1.6 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 36373 / Rsym value: 0.369 / % possible all: 27
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PDB_EXTRACT
2
dataextraction
ProDC
datacollection
XDS
datareduction
XSCALE
datascaling
SHELXD
phasing
SHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.5→29.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.243 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.248
3633
5 %
RANDOM
Rwork
0.206
-
-
-
all
0.208
71962
-
-
obs
0.208
71962
68.29 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.966 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
0 Å2
-0.09 Å2
2-
-
-0.04 Å2
0 Å2
3-
-
-
0.04 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→29.34 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3987
0
52
544
4583
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
4163
X-RAY DIFFRACTION
r_angle_refined_deg
1.522
1.943
5655
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.374
5
483
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.93
23.521
213
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.919
15
663
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.82
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.113
0.2
571
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3272
X-RAY DIFFRACTION
r_nbd_refined
0.197
0.2
2184
X-RAY DIFFRACTION
r_nbtor_refined
0.308
0.2
2821
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.175
0.2
446
X-RAY DIFFRACTION
r_metal_ion_refined
0.033
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.176
0.2
63
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.152
0.2
25
X-RAY DIFFRACTION
r_mcbond_it
1.178
1.5
2483
X-RAY DIFFRACTION
r_mcangle_it
1.469
2
3914
X-RAY DIFFRACTION
r_scbond_it
2.579
3
1951
X-RAY DIFFRACTION
r_scangle_it
3.578
4.5
1741
LS refinement shell
Resolution: 1.5→1.539 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.465
66
-
Rwork
0.386
1413
-
obs
-
1479
19.14 %
+
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