- PDB-2huh: Crystal structure of a duf2027 family protein (bt_2179) from bact... -
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Basic information
Entry
Database: PDB / ID: 2huh
Title
Crystal structure of a duf2027 family protein (bt_2179) from bacteroides thetaiotaomicron at 1.54 A resolution
Components
Putative DNA mismatch repair protein
Keywords
UNKNOWN FUNCTION / Putative dna mismatch repair protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information
Smr-associated-like / Domain of unknown function DUF2027 / Smr-associated-like superfamily / Domain of unknown function (DUF2027) / Smr domain / Smr domain / Smr domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology
Resolution: 1.5→30.002 Å / Num. obs: 23849 / % possible obs: 97.6 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 6.1
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.54-1.58
4.2
0.767
1
6679
1601
0.767
92.7
1.58-1.62
5.1
0.585
1.3
8414
1636
0.585
95.5
1.62-1.67
6.3
0.492
1.6
10108
1605
0.492
96.4
1.67-1.72
6.2
0.399
1.9
9841
1586
0.399
96.5
1.72-1.78
6.3
0.279
2.7
9529
1507
0.279
96.9
1.78-1.84
6.3
0.219
3.5
9410
1499
0.219
97.1
1.84-1.91
6.2
0.169
4.4
8927
1434
0.169
97.4
1.91-1.99
6.3
0.13
5.4
8647
1372
0.13
97
1.99-2.08
6.3
0.111
5.7
8418
1345
0.111
97.4
2.08-2.18
7.7
0.117
5.6
10001
1296
0.117
97.7
2.18-2.3
9.8
0.121
5.4
12188
1249
0.121
99.6
2.3-2.43
11.7
0.108
6
14110
1206
0.108
100
2.43-2.6
13.2
0.1
6.3
14809
1119
0.1
99.9
2.6-2.81
13.4
0.095
6.8
14174
1060
0.095
100
2.81-3.08
13.3
0.082
7.4
13447
1008
0.082
100
3.08-3.44
13.5
0.068
8.6
12015
890
0.068
100
3.44-3.98
13.2
0.062
9.9
10687
808
0.062
100
3.98-4.87
13
0.056
10.9
9145
704
0.056
100
4.87-6.89
12.5
0.051
11.6
7113
571
0.051
100
6.89-30.01
10.5
0.045
12.4
3719
353
0.045
98.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.54→30.002 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.722 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. MODEL REPRESENTS A PROTEOLYTIC FRAGMENT OF THE FULL-LENGTH PROTEIN, THOUGH THE EXACT BOUNDRIES ARE UNKOWN. RESIDUES 81-227 ARE MODELED BASED ON DENSITY. 5. UNKNOWN DENSITY NEAR ASP 89 WAS NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.192
1216
5.1 %
RANDOM
Rwork
0.166
-
-
-
obs
0.168
23764
97.38 %
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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: 13.411 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.1 Å2
0 Å2
0 Å2
2-
-
0.1 Å2
0 Å2
3-
-
-
-0.19 Å2
Refinement step
Cycle: LAST / Resolution: 1.54→30.002 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1164
0
1
163
1328
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
1254
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1121
X-RAY DIFFRACTION
r_angle_refined_deg
1.493
1.968
1727
X-RAY DIFFRACTION
r_angle_other_deg
0.742
3
2620
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.645
5
166
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.188
25.333
60
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.378
15
203
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
4.205
15
3
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
196
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1421
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
253
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
200
X-RAY DIFFRACTION
r_nbd_other
0.174
0.2
1100
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
618
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
790
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.191
0.2
126
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.197
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.192
0.2
49
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.162
0.2
17
X-RAY DIFFRACTION
r_mcbond_it
1.966
3
816
X-RAY DIFFRACTION
r_mcbond_other
0.429
3
303
X-RAY DIFFRACTION
r_mcangle_it
2.548
5
1255
X-RAY DIFFRACTION
r_scbond_it
4.366
8
542
X-RAY DIFFRACTION
r_scangle_it
6.096
11
462
LS refinement shell
Resolution: 1.539→1.579 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.328
75
-
Rwork
0.261
1506
-
obs
-
1581
91.07 %
Refinement TLS params.
Method: refined / Origin x: 2.257 Å / Origin y: 10.604 Å / Origin z: 53.878 Å
11
12
13
21
22
23
31
32
33
T
0.0812 Å2
0.0101 Å2
-0.0133 Å2
-
0.0311 Å2
-0.0022 Å2
-
-
0.0245 Å2
L
0.6646 °2
0.3927 °2
0.5166 °2
-
0.8039 °2
0.4366 °2
-
-
1.2147 °2
S
-0.0486 Å °
-0.0482 Å °
0.0458 Å °
0.0318 Å °
0.021 Å °
-0.013 Å °
-0.1017 Å °
-0.0553 Å °
0.0276 Å °
Refinement TLS group
Selection: ALL
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