- PDB-4obi: Crystal structure of a DUF1312 family protein (EF3258) from Enter... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4obi
Title
Crystal structure of a DUF1312 family protein (EF3258) from Enterococcus faecalis V583 at 1.73 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF07009 family / DUF1312 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 79 / 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 36-140 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6 Details: 30.0000% polyethylene glycol 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91837 Å / Relative weight: 1
Reflection
Resolution: 1.73→40.559 Å / Num. obs: 10218 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.033 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.25
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
1.73-1.79
0.684
1.9
2926
794
78.1
1.79-1.86
0.521
2.7
3897
992
99.1
1.86-1.95
0.352
3.7
4115
1104
98
1.95-2.05
0.218
6.2
4085
998
99.2
2.05-2.18
0.167
8.1
4161
1047
99.1
2.18-2.35
0.114
11.1
3892
1031
98.1
2.35-2.58
0.088
14.2
4111
1029
99.1
2.58-2.96
0.057
20.2
4234
1081
99.1
2.96-3.72
0.03
33.7
4001
1035
97.4
3.72
0.024
44.4
4124
1143
96.1
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
XSCALE
datascaling
REFMAC
5.7.0032
refinement
XDS
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.734→40.559 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.851 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF A ZINC (ZN) ION. 6. A TETRAETHYLENE GLYCOL (PG4) FRAGMENT FROM THE CRYOPROTECTION SOLUTION IS MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1992
485
4.7 %
RANDOM
Rwork
0.169
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obs
0.1704
10216
97 %
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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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