- PDB-2oz5: Crystal structure of Mycobacterium tuberculosis protein tyrosine ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2oz5
Title
Crystal structure of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB in complex with the specific inhibitor OMTS
Components
Phosphotyrosine protein phosphatase ptpb
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein tyrosine phosphatase in complex with small molecule inhibitor / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information
phosphatidylinositol trisphosphate phosphatase activity / biological process involved in interaction with host / protein serine/threonine phosphatase activity / phosphatase activity / protein dephosphorylation / protein tyrosine phosphatase activity / extracellular region Similarity search - Function
Tyrosine/serine-protein phosphatase IphP-type / Tyrosine phosphatase family / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1159 Å / Relative weight: 1
Reflection
Resolution: 2→50 Å / Num. obs: 34740 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.034 / Χ2: 0.814 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2-2.07
1.9
0.09
2839
0.706
1
80.8
2.07-2.15
2.2
0.076
3258
0.711
1
93
2.15-2.25
3
0.07
3453
0.828
1
97.4
2.25-2.37
3.7
0.064
3491
0.87
1
99.4
2.37-2.52
4.2
0.064
3558
1.029
1
100
2.52-2.71
4.2
0.05
3540
0.868
1
100
2.71-2.99
4.2
0.039
3572
0.786
1
100
2.99-3.42
4.2
0.031
3586
0.791
1
100
3.42-4.31
4.2
0.024
3633
0.745
1
100
4.31-50
4
0.021
3802
0.667
1
100
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Phasing
Phasing MR
Rfactor: 0.46 / Cor.coef. Fo:Fc: 0.472
Highest resolution
Lowest resolution
Rotation
3 Å
48.03 Å
Translation
3 Å
48.03 Å
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
MOLREP
phasing
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
ADSC
QUANTUM
datacollection
HKL-2000
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.98 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Some atoms in ARG 235 A, ARG 269 A, ARG 124 B, and ARG 258 B were modeled with zero occupancy leading to high RMS deviation values in these residues.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.249
1789
5.1 %
RANDOM
Rwork
0.189
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-
-
obs
0.192
34740
97.07 %
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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: 14.435 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.47 Å2
0 Å2
0 Å2
2-
-
-0.51 Å2
0 Å2
3-
-
-
0.04 Å2
Refinement step
Cycle: LAST / Resolution: 2→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4034
0
156
360
4550
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
4184
X-RAY DIFFRACTION
r_angle_refined_deg
1.511
2.008
5683
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
9.988
5
521
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.17
21.62
179
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.903
15
628
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.364
15
55
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
646
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
3209
X-RAY DIFFRACTION
r_nbd_refined
0.202
0.2
2033
X-RAY DIFFRACTION
r_nbtor_refined
0.305
0.2
2886
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.152
0.2
324
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.181
0.2
60
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.136
0.2
25
X-RAY DIFFRACTION
r_mcbond_it
0.737
1.5
2674
X-RAY DIFFRACTION
r_mcangle_it
1.225
2
4148
X-RAY DIFFRACTION
r_scbond_it
2.053
3
1696
X-RAY DIFFRACTION
r_scangle_it
3.217
4.5
1535
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.302
102
-
Rwork
0.18
1965
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obs
-
2067
79.56 %
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