Crystal structure of putative nucleic acid-binding lipoprotein (YP_001337197.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.46 A resolution
Components
putative nucleic acid-binding lipoprotein
Keywords
DNA BINDING PROTEIN / YP_001337197.1 / putative nucleic acid-binding lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Protein of unknown function, OB-fold-containing / tRNA_anti-like / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 10 CHAINS FORMING A DIMER OF STACKED PENTAMERIC RINGS. HOWEVER, QUATERNARY STRUCTURE ANALYSIS USING THE PISA SERVER AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A MONOMER AS THE LIKELY STABLE FORM.
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Components
#1: Protein
putativenucleicacid-bindinglipoprotein
Mass: 14601.099 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) Gene: KPN78578_35060, KPN_03535, YP_001337197.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6TEE6
Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT IS COMPRISED OF RESIDUES 23-154 OF THE FULL-LENGTH PROTEIN 1-154. IT WAS EXPRESSED ...THIS CONSTRUCT IS COMPRISED OF RESIDUES 23-154 OF THE FULL-LENGTH PROTEIN 1-154. IT 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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 31.0% polyethylene glycol 600, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9792 Å / Relative weight: 1
Reflection
Resolution: 2.46→29.881 Å / Num. obs: 68362 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 50.365 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 4.443
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
2.46-2.52
7.6
0.696
1.1
37475
4955
0.696
99.7
2.52-2.59
7.6
0.551
1.4
36830
4870
0.551
99.8
2.59-2.67
7.6
0.482
1.4
35803
4742
0.482
99.9
2.67-2.75
7.5
0.372
2
34809
4619
0.372
99.9
2.75-2.84
7.6
0.302
2.5
33735
4465
0.302
99.9
2.84-2.94
7.5
0.249
3.1
32710
4333
0.249
100
2.94-3.05
7.5
0.202
3.8
31592
4188
0.202
100
3.05-3.18
7.5
0.156
4.8
30439
4039
0.156
100
3.18-3.32
7.5
0.121
6.1
29123
3868
0.121
100
3.32-3.48
7.5
0.109
3.1
27873
3723
0.109
100
3.48-3.67
7.5
0.095
3
26529
3538
0.095
100
3.67-3.89
7.5
0.082
4.1
25103
3363
0.082
100
3.89-4.16
7.4
0.076
7.7
23373
3147
0.076
100
4.16-4.49
7.4
0.071
8.9
21882
2956
0.071
100
4.49-4.92
7.4
0.068
9.4
20286
2747
0.068
100
4.92-5.5
7.3
0.065
10.3
18059
2463
0.065
100
5.5-6.35
7.2
0.075
8.8
15824
2190
0.075
99.7
6.35-7.78
7.1
0.07
9.1
13310
1877
0.07
99.6
7.78-11
6.9
0.058
10.3
10277
1481
0.058
99.2
11-29.881
6.2
0.06
9.4
4964
798
0.06
93
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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
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.46→29.881 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.325 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.218 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.PEG (PEG600 FRAGMENTS) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.228
3458
5.1 %
RANDOM
Rwork
0.192
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-
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obs
0.194
68310
99.71 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
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