- PDB-2f22: CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTE... -
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Basic information
Entry
Database: PDB / ID: 2f22
Title
CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTEIN (BH3987) FROM BACILLUS HALODURANS AT 1.42 A RESOLUTION
Components
BH3987
Keywords
METAL BINDING PROTEIN / PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / Unknown
Function and homology information
Biological species
Bacillus halodurans (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å
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.
Resolution: 1.35→24.3 Å / Num. obs: 58327 / % possible obs: 98.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
% possible obs (%)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
1.42-1.46
91.8
2.9
0.484
1.5
3941
0.484
1.46-1.5
95.8
3.2
0.385
1.9
4047
0.385
1.5-1.54
98.1
3.5
0.326
2.1
3963
0.326
1.54-1.59
100
3.6
0.287
2.5
3993
0.287
1.59-1.64
100
3.6
0.248
3
3839
0.248
1.64-1.7
100
3.6
0.213
3.4
3749
0.213
1.7-1.76
100
3.6
0.191
3.8
3586
0.191
1.76-1.83
100
3.6
0.16
4.4
3485
0.16
1.83-1.91
100
3.6
0.139
5
3332
0.139
1.91-2.01
100
3.6
0.12
5.5
3203
0.12
2.01-2.12
100
6.7
0.138
5
3033
0.138
2.12-2.25
100
7.2
0.122
5.6
2915
0.122
2.25-2.4
99.9
7.3
0.108
6.4
2693
0.108
2.4-2.59
100
7.2
0.093
7.4
2564
0.093
2.59-2.84
100
7.2
0.083
8.3
2333
0.083
2.84-3.18
99.9
7.1
0.075
8.7
2140
0.075
3.18-3.67
99.8
7.1
0.066
9.8
1891
0.066
3.67-4.49
99.6
6.9
0.059
10.7
1633
0.059
4.49-6.35
99.4
6.7
0.065
9.6
1266
0.065
6.35-24.3
96.2
5.9
0.069
8.6
721
0.069
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
SCALA
datascaling
PDB_EXTRACT
1.601
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.42→23.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.778 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 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. NI ATOMS MODELED BASED ON ANOMALOUS AND DIFFERENCE MAPS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.182
2955
5.1 %
RANDOM
Rwork
0.157
-
-
-
all
0.158
-
-
-
obs
-
55316
98.65 %
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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: 6.73 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.14 Å2
0 Å2
0 Å2
2-
-
-0.33 Å2
0 Å2
3-
-
-
0.19 Å2
Refinement step
Cycle: LAST / Resolution: 1.42→23.59 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2305
0
3
412
2720
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2520
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1754
X-RAY DIFFRACTION
r_angle_refined_deg
1.432
1.963
3433
X-RAY DIFFRACTION
r_angle_other_deg
1.135
3
4324
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.577
5
329
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.812
24.545
121
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.235
15
499
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.659
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
380
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2799
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
498
X-RAY DIFFRACTION
r_nbd_refined
0.234
0.2
553
X-RAY DIFFRACTION
r_nbd_other
0.19
0.2
1802
X-RAY DIFFRACTION
r_nbtor_refined
0.187
0.2
1209
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
1219
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.174
0.2
302
X-RAY DIFFRACTION
r_metal_ion_refined
0.31
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.095
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.194
0.2
46
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.166
0.2
36
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.045
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
1.223
3
1496
X-RAY DIFFRACTION
r_mcbond_other
0.351
3
610
X-RAY DIFFRACTION
r_mcangle_it
2.127
5
2439
X-RAY DIFFRACTION
r_scbond_it
3.832
8
1062
X-RAY DIFFRACTION
r_scangle_it
5.339
11
969
LS refinement shell
Resolution: 1.419→1.455 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.287
190
-
Rwork
0.261
3678
-
obs
-
-
89.87 %
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
0.5585
-0.2065
-0.1544
1.49
0.4539
0.7245
0.0071
-0.0132
0.0067
-0.0052
-0.0116
0.0028
-0.0054
-0.0035
0.0045
0.0095
-0.0073
0.0098
0.0176
-0.0012
0.011
18.6106
4.1964
20.2861
2
0.7147
-0.2396
0.1308
2.2382
0.7073
2.6559
0.0524
0.0198
0.0116
0.0253
0.0198
-0.0307
0.0909
0.0462
-0.0722
0.0016
-0.009
0.003
0.0245
-0.0079
0.0358
15.9203
-4.0342
14.882
3
0.9356
0.639
0.5071
2.5269
1.5834
2.839
0.0134
0.0019
0.0115
0.0153
-0.0634
0.082
-0.0246
-0.0886
0.05
-0.0073
-0.0008
0.0093
0.0233
0.0023
0.0137
21.9094
8.9246
18.763
4
0.6679
0.0051
-0.2467
1.6673
0.9858
1.3661
-0.0073
-0.0043
0.026
0.0074
0.0026
-0.0676
0.0209
-0.0167
0.0048
0.0176
0.0097
0.0039
0.0251
0.0098
0.0316
36.7213
13.7296
15.9002
5
2.5435
1.2602
-0.1519
4.0584
-0.2753
1.8935
0.0019
0.0436
-0.114
-0.0877
0.0035
-0.1411
-0.0367
-0.0417
-0.0055
0.0451
0.0088
0.0357
0.0738
-0.0142
0.0514
41.3153
4.2039
7.6074
6
0.5179
-0.3471
-0.1996
5.9491
1.4692
0.9685
0.031
0.0143
-0.01
0.0189
-0.016
-0.1355
-0.0147
-0.0215
-0.015
-0.0004
-0.0024
0.0107
0.0253
0.0038
0.0159
31.1868
13.2832
17.3402
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: all
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
0 - 43
1 - 44
2
2
A
A
44 - 100
45 - 101
3
3
A
A
101 - 141
102 - 142
4
4
B
B
1 - 48
2 - 49
5
5
B
B
49 - 100
50 - 101
6
6
B
B
101 - 143
102 - 144
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