- PDB-2it9: Crystal structure of a protein with unknown function from DUF155 ... -
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Open data
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Basic information
Entry
Database: PDB / ID: 2it9
Title
Crystal structure of a protein with unknown function from DUF155 family (YP_292156.1) from Prochlorococcus sp. NATL2A at 1.80 A resolution
Components
Hypothetical protein
Keywords
Structural Genomics/Unknown function / YP_292156.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Protein of unknown function DUF1818 / Domain of unknown function (DUF1818) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta Similarity search - Domain/homology
BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Resolution: 1.8→67.884 Å / Num. obs: 56456 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 8
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
1.8-1.85
3.6
0.665
1.1
14813
4097
0.665
100
1.85-1.9
3.6
0.511
1.4
14630
4045
0.511
99.9
1.9-1.95
3.6
0.351
2
14250
3931
0.351
100
1.95-2.01
3.6
0.239
3
13669
3800
0.239
100
2.01-2.08
3.6
0.205
3.4
13439
3716
0.205
99.9
2.08-2.15
3.6
0.155
4.5
12936
3584
0.155
100
2.15-2.23
3.6
0.13
5.4
12439
3448
0.13
100
2.23-2.32
3.6
0.117
6
11997
3342
0.117
100
2.32-2.43
3.6
0.1
7.1
11483
3203
0.1
99.9
2.43-2.55
3.6
0.088
8
11005
3073
0.088
100
2.55-2.68
3.6
0.075
9.3
10438
2929
0.075
99.9
2.68-2.85
3.6
0.063
10.7
9856
2775
0.063
99.7
2.85-3.04
3.5
0.054
11.7
9205
2593
0.054
99.8
3.04-3.29
3.5
0.046
12.6
8548
2440
0.046
99.5
3.29-3.6
3.5
0.044
12.9
7813
2237
0.044
99.2
3.6-4.02
3.4
0.039
14.6
6875
2025
0.039
98.7
4.02-4.65
3.2
0.032
18.1
5725
1773
0.032
97.6
4.65-5.69
3.5
0.033
16.8
5367
1533
0.033
98.7
5.69-8.05
3.6
0.034
16.3
4334
1213
0.034
98.3
8.05-67.88
3.4
0.032
13.5
2371
699
0.032
96.3
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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
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→67.884 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.666 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113 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) ELECTRON DENSITY BETWEEN RESIDUES 94-96 ON CHAIN A WERE DISORDERED; THEREFORE THESE RESIDUES WERE NOT MODELED INTO THE STRUCTURE. 5) THREE MOLECULES OF TRIETHYLENE GLYCOL (PGE) USED AS A CRYOPROTECTANT (PEG-200), FOUR MOLECULES OF ETHYLENE GLYCOL (CRYOPROTECTANT); ONE MOLECULE OF TRIS HYDROXYMETHYLAMINOMETHANE (TRS); AND A CHLORIDE ANION FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.213
2857
5.1 %
RANDOM
Rwork
0.179
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-
-
obs
0.181
56272
99.29 %
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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
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