- PDB-4jd0: Structure of the inositol-1-phosphate CTP transferase from T. mar... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4jd0
Title
Structure of the inositol-1-phosphate CTP transferase from T. maritima.
Components
Nucleotidyl transferaseNucleotidyltransferase
Keywords
TRANSFERASE / alpha/beta motif of sugar nucleotidyltransferase
Function / homology
Function and homology information
Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / biosynthetic process / nucleotidyltransferase activity Similarity search - Function
Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.91 Å3/Da / Density % sol: 68.5 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.8 2.0 M ammonium phosphate and 100 mM LiCl buffered at pH 8.5 with 100 mM Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 1.8→115.47 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.877 / SU ML: 0.052 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.16606
1925
5 %
RANDOM
Rwork
0.11136
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obs
0.1141
36573
93.82 %
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all
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38500
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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: 31.767 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.64 Å2
0.32 Å2
0 Å2
2-
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0.64 Å2
0 Å2
3-
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-0.96 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→115.47 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1939
0
50
240
2229
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.024
0.02
2241
X-RAY DIFFRACTION
r_angle_refined_deg
2.354
1.995
3078
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.493
5
309
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.757
24.455
101
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.36
15
432
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.972
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.153
0.2
346
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
1685
X-RAY DIFFRACTION
r_rigid_bond_restr
8.052
3
2241
X-RAY DIFFRACTION
r_sphericity_free
46.379
5
89
X-RAY DIFFRACTION
r_sphericity_bonded
28.252
5
2330
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.42
100
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Rwork
0.36
1832
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obs
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65.45 %
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