- PDB-3bhn: Crystal structure of a dj-1/pfpi-like protein (shew_2856) from sh... -
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Basic information
Entry
Database: PDB / ID: 3bhn
Title
Crystal structure of a dj-1/pfpi-like protein (shew_2856) from shewanella loihica pv-4 at 1.76 A resolution
Components
ThiJ/PfpI domain protein
Keywords
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ThiJ/PfpI domain protein
Function and homology information
Biological species
Shewanella loihica PV-4 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
Resolution: 1.76→29.223 Å / Num. obs: 27863 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.35 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.14
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
1.76-1.82
0.806
2
26238
1
95.4
1.82-1.9
0.6
2.8
31636
1
100
1.9-1.98
0.436
4
26930
1
99.9
1.98-2.09
0.29
6.1
30581
1
100
2.09-2.22
0.193
8.8
28768
1
100
2.22-2.39
0.139
11.8
28798
1
100
2.39-2.63
0.101
15.3
29162
1
100
2.63-3.01
0.072
20
28919
1
99.9
3.01-3.78
0.05
27.6
28654
1
100
3.78-29.223
0.044
32.6
28499
1
99
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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
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
ADSC
Quantum
datacollection
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.76→29.223 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.797 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.091 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. 1,2-ETHANEDIOL MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19
1398
5 %
RANDOM
Rwork
0.162
-
-
-
obs
0.163
27782
99.88 %
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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: 18.478 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.59 Å2
0.3 Å2
0 Å2
2-
-
0.59 Å2
0 Å2
3-
-
-
-0.89 Å2
Refinement step
Cycle: LAST / Resolution: 1.76→29.223 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1604
0
12
204
1820
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
1728
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1133
X-RAY DIFFRACTION
r_angle_refined_deg
1.397
1.972
2360
X-RAY DIFFRACTION
r_angle_other_deg
0.984
3
2815
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.968
5
242
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.769
25.714
70
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.681
15
301
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.813
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
279
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1960
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
323
X-RAY DIFFRACTION
r_nbd_refined
0.213
0.2
351
X-RAY DIFFRACTION
r_nbd_other
0.192
0.2
1195
X-RAY DIFFRACTION
r_nbtor_refined
0.174
0.2
847
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
857
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.177
0.2
165
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.169
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.158
0.2
24
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.219
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
1.862
3
1185
X-RAY DIFFRACTION
r_mcbond_other
0.461
3
456
X-RAY DIFFRACTION
r_mcangle_it
2.502
5
1790
X-RAY DIFFRACTION
r_scbond_it
4.785
8
671
X-RAY DIFFRACTION
r_scangle_it
6.046
11
556
LS refinement shell
Resolution: 1.76→1.81 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.273
109
-
Rwork
0.218
1869
-
all
-
1978
-
obs
-
-
98.95 %
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
1.1771
-0.0202
0.3503
1.5381
-0.711
1.0973
0.0337
0.0231
-0.0758
-0.064
0.1154
0.1004
0.0917
-0.1528
-0.1491
-0.0127
-0.0107
-0.0453
-0.0462
0.0377
-0.0284
-8.4506
65.3131
23.1685
2
1.2614
0.421
-0.0549
1.2876
-0.3008
1.4684
0.0464
-0.1459
-0.0033
0.249
0.0081
-0.0895
-0.098
0.003
-0.0546
0.0152
-0.0024
-0.0538
-0.0514
0.014
-0.0479
2.6618
72.818
32.5279
3
0.9434
0.0503
0.4371
1.0057
-0.1668
0.8699
0.0701
0.1454
-0.0353
0.0364
-0.1076
-0.2168
0.092
0.1515
0.0375
-0.0278
0.0201
-0.0261
-0.0158
0.0127
0.005
11.1304
73.6973
18.9981
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
1 - 88
20 - 107
2
X-RAY DIFFRACTION
2
A
A
89 - 152
108 - 171
3
X-RAY DIFFRACTION
3
A
A
153 - 214
172 - 233
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