- PDB-2zqe: Crystal structure of the Smr domain of Thermus thermophilus MutS2 -
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Basic information
Entry
Database: PDB / ID: 2zqe
Title
Crystal structure of the Smr domain of Thermus thermophilus MutS2
Components
MutS2 protein
Keywords
DNA BINDING PROTEIN / alpha/beta / ATP-binding / DNA-binding / Nucleotide-binding
Function / homology
Function and homology information
mismatched DNA binding / negative regulation of DNA recombination / mismatch repair / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #110 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair protein MutS, C-terminal ...Ribosomal Protein S8; Chain: A, domain 1 - #110 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / Ribosomal Protein S8; Chain: A, domain 1 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.7→7.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.899 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22699
443
4.9 %
RANDOM
Rwork
0.18876
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-
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obs
0.19074
8597
100 %
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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: 11.168 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0.04 Å2
0 Å2
3-
-
-
-0.03 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→7.9 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
599
0
0
104
703
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.021
604
X-RAY DIFFRACTION
r_angle_refined_deg
1.066
2.005
814
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.9
5
79
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.456
21.923
26
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.44
15
108
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
7.149
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.066
0.2
97
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
448
X-RAY DIFFRACTION
r_nbd_refined
0.198
0.2
260
X-RAY DIFFRACTION
r_nbtor_refined
0.302
0.2
411
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.147
0.2
74
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.116
0.2
36
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.172
0.2
11
X-RAY DIFFRACTION
r_mcbond_it
0.676
1.5
399
X-RAY DIFFRACTION
r_mcangle_it
1.204
2
621
X-RAY DIFFRACTION
r_scbond_it
2.296
3
212
X-RAY DIFFRACTION
r_scangle_it
3.982
4.5
193
LS refinement shell
Resolution: 1.702→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.291
24
-
Rwork
0.19
597
-
obs
-
-
100 %
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