Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2
Components
Nucleoside triphosphatase nudI
Keywords
HYDROLASE / STRUCTURAL GENOMICS / ISFI / SURFACE ENTROPY REDUCTION / PSI-2 / PROTEIN STRUCTURE INITIATIVE / INTEGRATED CENTER FOR STRUCTURE AND FUNCTION INNOVATION / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID)
Function / homology
Function and homology information
dCTP diphosphatase / dTTP diphosphatase activity / dCTP diphosphatase activity / nucleotide diphosphatase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / cytoplasm Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 200nl of protein at 20mg/ml was mixed with 200nl of 0.1M Ammonium acetate, 0.1M Bis-Tris pH5.5, 17%w/v PEG10000 suspended over reservoir of 60 ul of 1.5M NaCl, vapor diffusion, sitting drop, temperature 293K
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2009
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Redundancy: 5.8 % / Av σ(I) over netI: 15.31 / Number: 138799 / Rmerge(I) obs: 0.234 / Χ2: 1.75 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 23944 / % possible obs: 95
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.88
50
99.8
1
0.239
1.87
8.4
3.88
4.88
100
1
0.212
1.749
8.9
3.39
3.88
100
1
0.218
1.823
8.8
3.08
3.39
100
1
0.244
1.907
8.5
2.86
3.08
100
1
0.261
1.839
8
2.69
2.86
100
1
0.27
1.989
7.2
2.55
2.69
99.8
1
0.275
1.953
6.6
2.44
2.55
99.8
1
0.279
1.818
6.1
2.35
2.44
99.9
1
0.272
1.807
5.8
2.27
2.35
100
1
0.282
1.655
5.5
2.2
2.27
99.7
1
0.279
1.876
5.3
2.13
2.2
99.8
1
0.275
1.637
5.1
2.08
2.13
99.9
1
0.278
1.735
4.9
2.03
2.08
99.8
1
0.292
1.563
4.6
1.98
2.03
99.4
1
0.289
1.405
4.3
1.94
1.98
99.2
1
0.323
1.32
3.9
1.9
1.94
95.5
1
0.334
1.138
3.3
1.86
1.9
89.4
1
0.344
1.023
2.8
1.83
1.86
76.1
1
0.307
0.9
2.2
1.8
1.83
41.6
1
0.358
0.894
1.6
Reflection
Resolution: 1.86→40 Å / Num. obs: 22053 / % possible obs: 97.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
% possible all
1.86-1.93
2
0.211
79.4
1.93-2
2.5
0.165
95.2
2-2.09
3
0.136
99.2
2.09-2.21
3.3
0.108
99.8
2.21-2.34
3.4
0.093
99.9
2.34-2.52
3.5
0.073
99.9
2.52-2.78
3.5
0.061
100
2.78-3.18
3.5
0.055
99.9
3.18-4.01
3.5
0.065
99.8
4.01-40
3.4
0.063
98.6
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
SERGUI
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
BALBES
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GRN
Resolution: 1.86→38.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.791 / SU ML: 0.1 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23348
1041
4.7 %
RANDOM
Rwork
0.16694
-
-
-
obs
0.17
20995
96.99 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 31.844 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.18 Å2
0 Å2
1.11 Å2
2-
-
0.18 Å2
0 Å2
3-
-
-
0.54 Å2
Refinement step
Cycle: LAST / Resolution: 1.86→38.06 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2262
0
0
204
2466
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2334
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
1605
X-RAY DIFFRACTION
r_angle_refined_deg
1.552
1.967
3171
X-RAY DIFFRACTION
r_angle_other_deg
1.196
3
3887
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.782
5
292
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.907
23.559
118
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.475
15
409
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.247
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
351
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2620
X-RAY DIFFRACTION
r_gen_planes_other
0.004
0.02
494
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.861→1.909 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.293
41
-
Rwork
0.204
1144
-
obs
-
-
73.15 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.8019
-0.0207
-0.1329
1.3597
0.2751
0.0984
-0.0635
-0.0453
-0.0454
0.1335
0.0328
0.1155
0.0448
0.0143
0.0307
0.03
0.004
0.0141
0.0278
0.0075
0.0124
-10.3441
14.0576
36.4897
2
1.79
-0.2267
-0.2736
1.7062
-0.1446
0.4223
-0.0323
0.1329
-0.0316
-0.2383
0.0222
0.1165
0.0235
0.0013
0.01
0.0556
-0.0097
-0.0243
0.0249
0.0001
0.0126
-8.6596
-1.456
56.7996
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-10 - 9999
2
X-RAY DIFFRACTION
2
B
-10 - 9999
+
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