- PDB-4raa: Crystal structure of a Putative exported protein (BF0058) from Ba... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4raa
Title
Crystal structure of a Putative exported protein (BF0058) from Bacteroides fragilis NCTC 9343 at 2.60 A resolution
Components
Putative exported protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF16288 family / DUF4934 / 6-bladed beta-propeller of YWTD superfamily / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Six-bladed beta-propeller, TolB-like / PHOSPHATE ION / Putative exported protein
Function and homology information
Biological species
Bacteroides fragilis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 23-383 OF THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.250M di-ammonium hydrogen phosphate, 22.1% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97947
1
3
0.97908
1
Reflection
Resolution: 2.6→61.243 Å / Num. obs: 14464 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.928 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.59
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.6-2.67
0.649
1
3110
1992
92.3
2.67-2.74
0.48
1.2
3052
1971
94.7
2.74-2.82
0.452
1.5
2885
1863
92.4
2.82-2.91
0.323
2
2853
1868
92.3
2.91-3.01
0.281
2.4
2449
1660
90.3
3.01-3.11
0.187
3.3
2751
1756
94.2
3.11-3.23
0.139
4.4
2658
1694
94.9
3.23-3.36
0.119
5.5
2469
1594
93
3.36-3.51
0.086
7.4
2371
1549
92.5
3.51-3.68
0.073
9.3
2055
1402
89.3
3.68-3.88
0.053
11.2
2174
1387
94
3.88-4.12
0.046
13.6
2063
1331
93.9
4.12-4.4
0.036
17
1893
1225
93.3
4.4-4.75
0.031
18.5
1773
1169
93.9
4.75-5.21
0.03
19.7
1633
1056
93.1
5.21-5.82
0.036
17.6
1561
997
94
5.82-6.72
0.045
15.5
1270
819
93.8
6.72-8.23
0.029
19.5
1059
707
90.2
8.23-11.64
0.02
31
871
556
91.9
11.64
0.014
39.8
445
285
89.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
XSCALE
January10, 2014BUILT=20140307
datascaling
REFMAC
5.7.0032
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.6→61.243 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.501 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.661 / ESU R Free: 0.316 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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. 5. PHOSPHATE ION (PO4) CRYSTALLIZATION SOLUTION IS MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2571
728
5 %
RANDOM
Rwork
0.214
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obs
0.2162
14460
96.88 %
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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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