- PDB-3k8r: Crystal structure of protein of unknown function (YP_427503.1) fr... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3k8r
Title
Crystal structure of protein of unknown function (YP_427503.1) from Rhodospirillum rubrum ATCC 11170 at 2.75 A resolution
Components
Uncharacterized protein
Keywords
Structural Genomics / Unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Uncharacterised protein PF10387, DUF2442 / Protein of unknown function DUF2442 / Protein of unknown function (DUF2442) / NE0471 N-terminal domain-like / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Rhodospirillum rubrum ATCC 11170 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
CRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.
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Components
#1: Protein
Uncharacterizedprotein
Mass: 13418.640 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria) Strain: ATCC 11170 / NCIB 8255 / Gene: Rru_A2416 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2RRM9
Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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.
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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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20.0000% PEG-6000, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97932
1
Reflection
Resolution: 2.75→28.855 Å / Num. obs: 7459 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 75.246 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.75-2.85
0.616
1.5
2732
1391
1
94.9
2.85-2.96
0.43
2.2
2627
1353
1
99.2
2.96-3.1
0.272
3.2
2878
1481
1
98.3
3.1-3.26
0.197
4.4
2736
1393
1
98.7
3.26-3.46
0.123
6.2
2717
1396
1
98.5
3.46-3.73
0.076
9.6
2792
1424
1
98.5
3.73-4.1
0.069
10.9
2756
1407
1
97.8
4.1-4.69
0.046
14.4
2761
1410
1
98.1
4.69-5.88
0.045
16
2726
1393
1
97.9
5.88-28.855
0.034
19.2
2836
1442
1
97.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.75→28.855 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 24.86 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.278 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.235
344
4.6 %
RANDOM
Rwork
0.213
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obs
0.214
7458
99.52 %
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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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