- PDB-4r1k: Crystal structure of a NTF2-like protein (EUBSIR_01394) from Euba... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4r1k
Title
Crystal structure of a NTF2-like protein (EUBSIR_01394) from Eubacterium siraeum DSM 15702 at 2.56 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NTF2-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Protein of unknown function DUF5104 / Domain of unknown function (DUF5104) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Eubacterium siraeum (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.56 Å
Mass: 18.015 Da / Num. of mol.: 4 / 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 30-166 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M magnesium acetate, 30.0% 2-methyl-2,4-pentanediol, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
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
0.97939
1
2
0.91837
1
3
0.97882
1
Reflection
Resolution: 2.56→42.844 Å / Num. obs: 11309 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.294 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.16
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
2.56-2.65
0.652
2.1
4245
1109
97.5
2.65-2.76
0.544
2.5
4217
1153
97.8
2.76-2.88
0.352
3.6
3713
1047
95.7
2.88-3.03
0.24
5.4
4488
1128
99
3.03-3.22
0.158
7.6
4513
1142
99.3
3.22-3.47
0.115
10.2
4444
1142
98.3
3.47-3.82
0.09
12.6
4263
1145
98.7
3.82-4.37
0.06
16.8
3857
1087
94.4
4.37-5.48
0.053
19.8
4446
1143
98.6
5.48
0.051
20.4
4287
1172
96.1
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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
datascaling
REFMAC
5.7.0032
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.56→42.844 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 29.488 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.357 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. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2989
543
4.8 %
RANDOM
Rwork
0.2528
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obs
0.2551
10762
97.77 %
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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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