- PDB-3b81: Crystal structure of predicted DNA-binding transcriptional regula... -
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Basic information
Entry
Database: PDB / ID: 3b81
Title
Crystal structure of predicted DNA-binding transcriptional regulator of TetR/AcrR family (NP_350189.1) from Clostridium acetobutylicum at 2.10 A resolution
Components
Transcriptional regulator, AcrR family
Keywords
TRANSCRIPTION REGULATOR / NP_350189.1 / predicted DNA-binding transcriptional regulator of TetR/AcrR family / Bacterial regulatory proteins / tetR family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Transcription regulation
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence details
REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: NANODROP, 25.0% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.1→29.988 Å / Num. obs: 17429 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 6
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
2.1-2.15
6.8
0.983
0.7
8668
1282
0.983
100
2.15-2.21
6.8
0.771
0.9
8210
1208
0.771
100
2.21-2.28
6.3
0.741
0.5
7544
1198
0.741
100
2.28-2.35
6.8
0.501
1.5
7866
1165
0.501
100
2.35-2.42
6.7
0.445
1.7
7703
1144
0.445
100
2.42-2.51
6.7
0.32
2.3
7304
1085
0.32
100
2.51-2.6
6.7
0.276
2.7
7104
1056
0.276
100
2.6-2.71
6.5
0.217
3.3
6553
1012
0.217
100
2.71-2.83
6.7
0.171
4.3
6606
989
0.171
100
2.83-2.97
6.7
0.14
5.3
6231
936
0.14
100
2.97-3.13
6.6
0.102
6.9
5876
891
0.102
100
3.13-3.32
6.5
0.075
9.3
5616
858
0.075
100
3.32-3.55
6.3
0.07
9.2
5107
813
0.07
100
3.55-3.83
6.3
0.058
10.8
4696
744
0.058
100
3.83-4.2
6.1
0.051
12.4
4290
701
0.051
100
4.2-4.7
6
0.051
12
3862
644
0.051
100
4.7-5.42
5.5
0.066
9.1
3182
575
0.066
100
5.42-6.64
6.1
0.069
8.8
3002
494
0.069
100
6.64-9.39
6.2
0.034
18.5
2414
390
0.034
100
9.39-29.988
5.4
0.027
23.2
1322
244
0.027
97.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
ADSC
Quantum
datacollection
MOSFLM
datareduction
SHELXD
phasing
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→29.988 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 11.79 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.155 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 0-5, 96-106, AND 200-202 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.234
882
5.1 %
RANDOM
Rwork
0.203
-
-
-
obs
0.204
17389
99.9 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 41.914 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.65 Å2
0 Å2
0 Å2
2-
-
-1.65 Å2
0 Å2
3-
-
-
3.29 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→29.988 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1468
0
13
82
1563
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1543
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
1050
X-RAY DIFFRACTION
r_angle_refined_deg
1.514
1.963
2084
X-RAY DIFFRACTION
r_angle_other_deg
1.298
3
2586
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.409
5
193
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.353
25.634
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.533
15
288
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.909
15
3
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
238
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1684
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
305
X-RAY DIFFRACTION
r_nbd_refined
0.176
0.2
302
X-RAY DIFFRACTION
r_nbd_other
0.124
0.2
898
X-RAY DIFFRACTION
r_nbtor_refined
0.159
0.2
740
X-RAY DIFFRACTION
r_nbtor_other
0.072
0.2
691
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.096
0.2
48
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.128
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.135
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.089
0.2
15
X-RAY DIFFRACTION
r_mcbond_it
1.621
3
927
X-RAY DIFFRACTION
r_mcbond_other
0.329
3
375
X-RAY DIFFRACTION
r_mcangle_it
3.054
5
1501
X-RAY DIFFRACTION
r_scbond_it
4.707
8
633
X-RAY DIFFRACTION
r_scangle_it
7.034
11
577
LS refinement shell
Resolution: 2.1→2.155 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.292
56
-
Rwork
0.274
1223
-
all
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1279
-
obs
-
-
99.92 %
Refinement TLS params.
Method: refined / Origin x: 20.579 Å / Origin y: 29.953 Å / Origin z: 25.176 Å
11
12
13
21
22
23
31
32
33
T
0.073 Å2
-0.0517 Å2
-0.0758 Å2
-
0.0676 Å2
0.0077 Å2
-
-
0.0024 Å2
L
3.2687 °2
2.3471 °2
0.5889 °2
-
2.86 °2
1.0913 °2
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-
0.4864 °2
S
-0.2318 Å °
0.2803 Å °
0.375 Å °
-0.3561 Å °
0.059 Å °
0.5192 Å °
0.0273 Å °
-0.1497 Å °
0.1728 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
6 - 95
7 - 96
2
X-RAY DIFFRACTION
1
A
A
107 - 199
108 - 200
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