- PDB-2o3l: Crystal structure of a duf1048 protein with a left-handed superhe... -
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Basic information
Entry
Database: PDB / ID: 2o3l
Title
Crystal structure of a duf1048 protein with a left-handed superhelix fold (bce_3448) from bacillus cereus atcc 10987 at 2.05 A resolution
Components
Hypothetical protein
Keywords
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Uncharacterised conserved protein UCP029876 / Protein of unknown function (DUF1048) / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological species
Bacillus cereus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE RESULTS OF SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE MONOMER AS A BIOLOGICALLY 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 (0) FOLLOWED BY RESIDUE 14 OF THE TARGET SEQUENCE.
THE RESULTS OF SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
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Components
#1: Protein
Hypotheticalprotein /
Mass: 9897.275 Da / Num. of mol.: 2 / Fragment: residues 14-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: NP_979748.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q734F7
Resolution: 1.999→29.298 Å / Num. obs: 14352 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 31.23 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 6.4
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.05-2.1
5.1
0.635
1.1
5308
1040
0.635
99.3
2.1-2.16
5.2
0.493
1.4
5217
1006
0.493
99.6
2.16-2.22
5.2
0.39
1.8
5119
989
0.39
99.6
2.22-2.29
5.2
0.301
2.3
4911
944
0.301
99.8
2.29-2.37
5.2
0.239
3
4965
949
0.239
99.9
2.37-2.45
5.3
0.19
3.7
4787
907
0.19
100
2.45-2.54
5.3
0.156
4.5
4563
860
0.156
100
2.54-2.65
5.4
0.126
5.6
4523
842
0.126
100
2.65-2.76
5.4
0.112
6.3
4417
820
0.112
100
2.76-2.9
5.4
0.09
7.8
4185
774
0.09
100
2.9-3.06
5.4
0.075
9.2
3996
743
0.075
100
3.06-3.24
5.4
0.056
12
3767
698
0.056
100
3.24-3.47
5.3
0.053
12.2
3539
662
0.053
100
3.47-3.74
5.3
0.051
11.5
3284
616
0.051
100
3.74-4.1
5.2
0.045
12.8
3068
589
0.045
100
4.1-4.58
5.3
0.037
15.8
2759
523
0.037
100
4.58-5.29
5.1
0.042
12.3
2391
466
0.042
100
5.29-6.48
5
0.045
12.8
2003
403
0.045
100
6.48-9.17
4.8
0.04
7.2
1576
331
0.04
100
9.17-29.3
4.2
0.041
9.5
792
190
0.041
96.2
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.05→29.298 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.2 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.154 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 0.70 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO SULFATE MOLECULES FROM CRYSTALLIZATION SOLUTION ARE INCLUDED IN THE MODEL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.227
723
5 %
RANDOM
Rwork
0.184
-
-
-
obs
0.186
14319
99.82 %
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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: 39.551 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.87 Å2
0.43 Å2
0 Å2
2-
-
0.87 Å2
0 Å2
3-
-
-
-1.3 Å2
Refinement step
Cycle: LAST / Resolution: 2.05→29.298 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1263
0
23
106
1392
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1359
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1199
X-RAY DIFFRACTION
r_angle_refined_deg
1.501
1.95
1841
X-RAY DIFFRACTION
r_angle_other_deg
0.858
3
2776
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.699
5
178
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.524
25.714
70
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.636
15
222
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
9.518
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
193
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1561
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
281
X-RAY DIFFRACTION
r_nbd_refined
0.222
0.2
350
X-RAY DIFFRACTION
r_nbd_other
0.169
0.2
1214
X-RAY DIFFRACTION
r_nbtor_refined
0.192
0.2
687
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
771
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.154
0.2
82
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.18
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.222
0.2
42
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.097
0.2
7
X-RAY DIFFRACTION
r_mcbond_it
2.487
3
858
X-RAY DIFFRACTION
r_mcbond_other
0.658
3
350
X-RAY DIFFRACTION
r_mcangle_it
3.489
5
1320
X-RAY DIFFRACTION
r_scbond_it
6.955
8
579
X-RAY DIFFRACTION
r_scangle_it
8.363
11
514
LS refinement shell
Resolution: 2.051→2.104 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.25
52
-
Rwork
0.253
987
-
obs
-
1039
99.52 %
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
4.3917
2.614
1.4675
7.0469
0.3711
2.5965
-0.0129
-0.2521
-0.0251
0.3783
-0.0042
-0.078
-0.1419
0.0081
0.0171
-0.1977
-0.0217
0.0194
-0.186
0.0451
-0.2175
-8.9251
27.1319
5.2546
2
0.3798
0.5539
-1.5429
1.3496
-1.3247
7.8496
0.0127
-0.0355
0.0292
0.1032
-0.0493
0.0419
-0.3734
0.031
0.0366
-0.1838
0.024
0.0039
-0.1666
-0.005
-0.132
-22.9839
17.2809
16.717
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
13 - 95
1 - 83
2
2
B
B
14 - 94
2 - 82
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