- PDB-3iee: Crystal structure of an alpha helical protein (BF3319) from Bacte... -
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Basic information
Entry
Database: PDB / ID: 3iee
Title
Crystal structure of an alpha helical protein (BF3319) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Components
Putative exported protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / YP_212931.1 / hypothetical protein BF3319 from Bacteroides fragilis / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Uncharacterised protein PF12889, C-terminal DUF3829 / Uncharacterised protein PF12889, N-terminal DUF3829 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Putative exported protein
Function and homology information
Biological species
Bacteroides fragilis NCTC 9343 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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. THE CLONED CONSTRUCT CONTAINS RESIDUES 18-286 OF THE FULL LENGTH PROTEIN.
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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 30.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97918 Å / Relative weight: 1
Reflection
Resolution: 1.7→29.26 Å / Num. obs: 30021 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.456 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11.1
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
1.7-1.74
4.4
0.66
1.2
9281
2089
0.66
96.1
1.74-1.79
4.8
0.585
1.3
10331
2136
0.585
99.2
1.79-1.84
4.9
0.459
1.7
10104
2083
0.459
99.5
1.84-1.9
4.9
0.388
2
9735
2000
0.388
99.1
1.9-1.96
4.9
0.295
2.6
9566
1955
0.295
99.2
1.96-2.03
4.9
0.23
3.4
9160
1880
0.23
99.4
2.03-2.11
4.9
0.183
4.2
8979
1841
0.183
99.6
2.11-2.19
4.9
0.149
5
8678
1770
0.149
99.9
2.19-2.29
4.9
0.131
5.7
8292
1695
0.131
99.7
2.29-2.4
4.9
0.117
6.2
7927
1626
0.117
99.8
2.4-2.53
4.8
0.108
6.8
7613
1570
0.108
99.8
2.53-2.69
4.9
0.098
7.4
7150
1471
0.098
99.9
2.69-2.87
4.8
0.089
8
6769
1397
0.089
99.8
2.87-3.1
4.8
0.082
8.2
6254
1298
0.082
100
3.1-3.4
4.8
0.066
9.6
5799
1207
0.066
100
3.4-3.8
4.7
0.057
10.9
5244
1110
0.057
100
3.8-4.39
4.7
0.055
11.5
4581
973
0.055
100
4.39-5.38
4.6
0.057
11.4
3912
856
0.057
99.9
5.38-7.6
4.4
0.064
9.8
2932
669
0.064
100
7.6-29.26
3.9
0.046
12.2
1554
395
0.046
98.1
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.7→29.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 3.964 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.1 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYO SOLUTION WERE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.192
1517
5.1 %
RANDOM
Rwork
0.164
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obs
0.166
29976
99.18 %
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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
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