- PDB-2re7: Crystal structure of a pyridoxamine 5'-phosphate oxidase related ... -
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Basic information
Entry
Database: PDB / ID: 2re7
Title
Crystal structure of a pyridoxamine 5'-phosphate oxidase related protein (psyc_0186) from psychrobacter arcticus 273-4 at 2.50 A resolution
Components
Uncharacterized protein
Keywords
OXIDOREDUCTASE / General stress protein cog3871 / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
General stress protein, FMN-binding split barrel domain / Pyridoxamine 5'-phosphate oxidase like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Pyrid_ox_like domain-containing protein
Function and homology information
Biological species
Psychrobacter arcticus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
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 FOLLOWED BY THE TARGET SEQUENCE.
Resolution: 2.5→28.433 Å / Num. obs: 8894 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 75.19 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 4.2
Reflection shell
Rmerge(I) obs: 0.01 / Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.5-2.56
7.4
0.7
4683
636
1.046
100
2.56-2.64
7.4
0.9
4725
637
0.795
100
2.64-2.71
7.3
1.3
4449
607
0.574
100
2.71-2.8
7.4
1.6
4441
603
0.449
100
2.8-2.89
7.4
2.3
4159
565
0.317
100
2.89-2.99
7.4
2.6
4117
557
0.258
100
2.99-3.1
7.4
3.9
4000
544
0.182
100
3.1-3.23
7.3
5
3774
518
0.139
100
3.23-3.37
7.3
5.6
3615
497
0.112
100
3.37-3.54
7.3
6.4
3538
487
0.101
100
3.54-3.73
7.2
7.3
3250
449
0.084
100
3.73-3.95
7.2
7.6
3255
452
0.074
100
3.95-4.23
7
7.8
2809
399
0.071
100
4.23-4.56
7
8.1
2753
395
0.073
100
4.56-5
6.8
6.8
2392
352
0.078
100
5-5.59
7
9
2311
331
0.069
100
5.59-6.45
6.8
9.3
1964
287
0.065
100
6.45-7.91
6.8
9.4
1772
260
0.063
100
7.91-11.18
6.3
6
1248
198
0.059
100
11.18-28.433
5.7
7.5
678
120
0.066
95.3
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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
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.5→28.433 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.7 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE IONS (SO4) FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 5. THE ELECTRON DENSITIES FOR RESIDUES 134-164 ARE DISORDERED, AND THESE RESIDUES WERE NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.226
424
4.8 %
RANDOM
Rwork
0.191
-
-
-
obs
0.192
8885
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: MASK
Displacement parameters
Biso mean: 42.729 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.76 Å2
0 Å2
0 Å2
2-
-
-1.76 Å2
0 Å2
3-
-
-
3.52 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→28.433 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1019
0
10
24
1053
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
1048
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
659
X-RAY DIFFRACTION
r_angle_refined_deg
1.645
1.936
1428
X-RAY DIFFRACTION
r_angle_other_deg
1.123
3
1629
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.696
5
131
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.902
26.667
48
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.239
15
171
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.761
15
1
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
161
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1168
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
189
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.3
194
X-RAY DIFFRACTION
r_nbd_other
0.162
0.3
630
X-RAY DIFFRACTION
r_nbtor_refined
0.178
0.5
477
X-RAY DIFFRACTION
r_nbtor_other
0.093
0.5
563
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.167
0.5
59
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.167
0.3
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.16
0.3
33
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.161
0.5
11
X-RAY DIFFRACTION
r_mcbond_it
1.941
3
717
X-RAY DIFFRACTION
r_mcbond_other
0.37
3
266
X-RAY DIFFRACTION
r_mcangle_it
3.094
5
1061
X-RAY DIFFRACTION
r_scbond_it
5.367
8
440
X-RAY DIFFRACTION
r_scangle_it
7.797
11
367
LS refinement shell
Resolution: 2.5→2.565 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.471
27
-
Rwork
0.401
608
-
all
-
635
-
obs
-
-
99.84 %
Refinement TLS params.
Method: refined / Origin x: 51.1702 Å / Origin y: 22.5969 Å / Origin z: 22.1508 Å
11
12
13
21
22
23
31
32
33
T
0.0415 Å2
-0.045 Å2
0.0593 Å2
-
-0.0125 Å2
0.0116 Å2
-
-
0.0183 Å2
L
3.0044 °2
-0.9888 °2
1.5357 °2
-
6.0234 °2
-3.2598 °2
-
-
4.2878 °2
S
0.0878 Å °
-0.3171 Å °
0.256 Å °
0.7177 Å °
-0.0701 Å °
0.3111 Å °
-0.5163 Å °
-0.0612 Å °
-0.0177 Å °
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