- PDB-2q03: Crystal structure of uncharacterized protein (YP_563039.1) from S... -
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Basic information
Entry
Database: PDB / ID: 2q03
Title
Crystal structure of uncharacterized protein (YP_563039.1) from Shewanella denitrificans OS217 at 1.80 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / YP_563039.1 / uncharacterized protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
SO1590-like / Protein of unknown function DUF3224 / SO1590-like superfamily / Protein of unknown function (DUF3224) / AOC barrel-like / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological species
Shewanella denitrificans OS217 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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 (0) FOLLOWED BY THE TARGET SEQUENCE.
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97926
1
3
0.97904
1
Reflection
Resolution: 1.8→29.161 Å / Num. obs: 46034 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 29.12 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.64
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.8-1.86
0.466
2.53
30204
8062
1
99.2
1.86-1.94
0.335
3.6
35497
9317
1
100
1.94-2.03
0.226
5.4
33853
8850
1
100
2.03-2.13
0.166
7.3
31048
8108
1
100
2.13-2.27
0.13
9.4
34784
9154
1
99.9
2.27-2.44
0.106
11.2
31936
8396
1
100
2.44-2.69
0.082
14
33635
8876
1
100
2.69-3.07
0.064
17.9
31793
8502
1
100
3.07-3.87
0.052
21.5
32350
8740
1
99.9
3.87-29.16
0.041
23.4
32335
8727
1
99.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.161 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.686 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.078 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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. TWO GLYCEROL MOLECULES ARE MODELED IN THE STRUCTURE. 5. RESIDUES 1 TO 4 IN SUBUNIT A AND B, RESIDUES 156 AND 137 IN SUBUNIT B ARE DISORDERED AND NOT MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.183
2322
5.1 %
RANDOM
Rwork
0.167
-
-
-
obs
0.168
45976
99.85 %
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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: 31.343 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.02 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.161 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2008
0
12
246
2266
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
2187
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
1863
X-RAY DIFFRACTION
r_angle_refined_deg
1.783
1.913
2973
X-RAY DIFFRACTION
r_angle_other_deg
0.851
3
4331
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.986
5
288
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.989
25.14
107
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.245
15
341
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.671
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
322
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2581
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
478
X-RAY DIFFRACTION
r_nbd_refined
0.168
0.3
306
X-RAY DIFFRACTION
r_nbd_other
0.172
0.3
1849
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.5
1021
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.5
1429
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.212
0.5
304
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.106
0.3
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.15
0.3
20
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.259
0.5
16
X-RAY DIFFRACTION
r_symmetry_hbond_other
0.013
0.5
1
X-RAY DIFFRACTION
r_mcbond_it
2.321
3
1417
X-RAY DIFFRACTION
r_mcbond_other
0.507
3
586
X-RAY DIFFRACTION
r_mcangle_it
3.303
5
2192
X-RAY DIFFRACTION
r_scbond_it
5.539
8
885
X-RAY DIFFRACTION
r_scangle_it
8.185
11
781
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.253
164
-
Rwork
0.217
3156
-
obs
-
3320
99.4 %
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
1.7551
-1.5802
-0.3702
3.3636
-0.6308
1.0186
-0.0557
-0.1515
-0.3282
-0.0296
0.0371
-0.1064
0.0192
-0.0547
0.0186
-0.1143
0.039
0.0141
-0.0937
0.0394
-0.0547
58.591
14.911
4.096
2
2.2009
-1.9071
-0.3934
4.6173
0.1757
0.5817
-0.1381
-0.3411
0.0468
0.468
0.1663
-0.1089
-0.1431
-0.1291
-0.0282
0.0233
0.1098
-0.0062
0.0052
-0.0019
-0.19
49.988
35.059
9.197
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
5 - 137
6 - 138
2
X-RAY DIFFRACTION
2
B
B
5 - 135
6 - 136
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