- PDB-3kwr: Crystal structure of Putative RNA-binding protein (NP_785364.1) f... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3kwr
Title
Crystal structure of Putative RNA-binding protein (NP_785364.1) from LACTOBACILLUS PLANTARUM at 1.45 A resolution
Components
Putative RNA-binding protein
Keywords
RNA BINDING PROTEIN / Putative RNA-binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Mass: 18.015 Da / Num. of mol.: 218 / 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.
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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.8000M (NH4)2SO4, 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: 0.97911 Å / Relative weight: 1
Reflection
Resolution: 1.45→29.67 Å / Num. obs: 40229 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.746 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.58
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
1.45-1.5
0.592
1.6
15319
6918
90.3
1.5-1.56
0.417
2.5
18639
7539
96.3
1.56-1.63
0.336
3.1
19394
7550
96.7
1.63-1.72
0.22
4.8
21155
7968
97.2
1.72-1.83
0.14
7.6
21186
7746
97.4
1.83-1.97
0.091
11.6
21255
7541
97.3
1.97-2.17
0.058
17.5
22190
7751
98
2.17-2.48
0.058
24.9
31341
7582
98.4
2.48-3.12
0.044
36
43910
7728
99
3.12
0.025
53.8
45405
7844
99.1
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Phasing
Phasing
Method: SAD
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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
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.45→29.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.892 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.SULPHATE ANION (SO4) FROM CRYSTALLIZATION AND GLYCEROL MOLECULE (GOL) FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.181
2017
5 %
RANDOM
Rwork
0.163
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obs
0.164
40213
99.67 %
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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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