- PDB-2hq7: Crystal structure of Protein related to general stress protein 26... -
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Basic information
Entry
Database: PDB / ID: 2hq7
Title
Crystal structure of Protein related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NP_350077.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.00 A resolution
Components
Protein, related to general stress protein 26(GS26) of B.subtilis
Keywords
OXIDOREDUCTASE / NP_350077.1 / Protein related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Protein, related to general stress protein 26(GS26) of B.subtilis (Pyridoxinephosphate oxidase family)
Function and homology information
Biological species
Clostridium acetobutylicum (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
Journal: To be published Title: Crystal structure of Protein related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NP_350077.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG)
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.
A: Protein, related to general stress protein 26(GS26) of B.subtilis B: Protein, related to general stress protein 26(GS26) of B.subtilis hetero molecules
A: Protein, related to general stress protein 26(GS26) of B.subtilis B: Protein, related to general stress protein 26(GS26) of B.subtilis hetero molecules
A: Protein, related to general stress protein 26(GS26) of B.subtilis B: Protein, related to general stress protein 26(GS26) of B.subtilis hetero molecules
Resolution: 2→29.235 Å / Num. obs: 19245 / % possible obs: 93.1 % / Biso Wilson estimate: 33.345 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.87
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique all
Diffraction-ID
% possible all
2-2.07
0.392
2
5761
2980
1
81.9
2.07-2.15
0.326
2.4
6272
3218
1
88.2
2.15-2.25
0.256
3
6692
3417
1
90.4
2.25-2.37
0.228
3.3
6723
3442
1
91.7
2.37-2.52
0.173
4.2
6850
3501
1
93
2.52-2.71
0.143
5.1
6735
3457
1
94.8
2.71-2.99
0.092
7.3
7202
3698
1
96.7
2.99-3.42
0.055
11
7045
3628
1
98.3
3.42-29.235
0.035
16.2
7103
3660
1
99.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0019
refinement
XSCALE
datascaling
PDB_EXTRACT
2
dataextraction
XDS
datareduction
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→29.235 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.679 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.18 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES A1, A143-145, B1, AND B144-145 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. EDO AND CL FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.242
985
5.1 %
RANDOM
Rwork
0.191
-
-
-
all
0.193
-
-
-
obs
0.19347
19244
99.59 %
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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: 31.614 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.97 Å2
0 Å2
-0.5 Å2
2-
-
3.14 Å2
0 Å2
3-
-
-
-1.57 Å2
Refinement step
Cycle: LAST / Resolution: 2→29.235 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2274
0
18
141
2433
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2349
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1589
X-RAY DIFFRACTION
r_angle_refined_deg
1.41
1.953
3167
X-RAY DIFFRACTION
r_angle_other_deg
0.832
3
3879
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.313
5
283
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.026
24.717
106
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.859
15
423
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.288
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
347
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2562
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
475
X-RAY DIFFRACTION
r_nbd_refined
0.188
0.2
435
X-RAY DIFFRACTION
r_nbd_other
0.194
0.2
1575
X-RAY DIFFRACTION
r_nbtor_refined
0.188
0.2
1124
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
1327
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.18
0.2
136
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.175
0.2
17
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.174
0.2
32
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.167
0.2
15
X-RAY DIFFRACTION
r_mcbond_it
2.616
3
1449
X-RAY DIFFRACTION
r_mcbond_other
0.608
3
577
X-RAY DIFFRACTION
r_mcangle_it
3.575
5
2268
X-RAY DIFFRACTION
r_scbond_it
6.24
8
1064
X-RAY DIFFRACTION
r_scangle_it
7.717
11
898
LS refinement shell
Resolution: 2→2.051 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.281
66
-
Rwork
0.264
1326
-
obs
-
1392
97.21 %
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
0.9959
-0.7125
-0.4292
0.7537
0.0377
0.7719
-0.0276
-0.0767
0.055
0.0229
-0.0229
-0.0565
-0.0319
0.0469
0.0505
-0.0072
-0.0104
-0.0049
-0.0402
0.0341
-0.0189
-12.61
2.764
32.277
2
1.627
-0.1091
-0.3088
0.4115
0.5681
1.4238
-0.0251
-0.0562
0.0705
-0.1281
-0.0359
0.0668
-0.0128
0.0418
0.0609
0.0183
0.0066
-0.018
-0.1205
0.0162
0.0028
-7.966
-5.429
12.888
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
2 - 142
3 - 143
2
2
B
B
2 - 143
3 - 144
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