- PDB-3f14: Crystal structure of NTF2-like protein of unknown function (YP_68... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3f14
Title
Crystal structure of NTF2-like protein of unknown function (YP_680363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.45 A resolution
Components
uncharacterized NTF2-like protein
Keywords
structural genomics / unknown function / YP_680363.1 / NTF2-like protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / TRIETHYLENE GLYCOL / SnoaL-like domain-containing protein
Function and homology information
Biological species
Cytophaga hutchinsonii ATCC 33406 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.45→25.933 Å / Num. obs: 20633 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.16 % / Biso Wilson estimate: 17.008 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.58
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.45-1.5
0.538
2.5
13549
3671
1
98.8
1.5-1.56
0.377
3.6
14859
3965
1
99.8
1.56-1.63
0.266
5
14450
3839
1
99.8
1.63-1.72
0.187
6.9
15535
4101
1
99.8
1.72-1.83
0.132
9.6
15078
3971
1
99.9
1.83-1.97
0.082
14.5
14858
3907
1
99.9
1.97-2.17
0.054
21.7
14853
3892
1
99.8
2.17-2.48
0.041
26.6
14744
3850
1
99.7
2.48-3.12
0.032
33.5
14887
3872
1
99.6
3.12-25.933
0.025
41.8
14983
3931
1
99.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
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: 1.45→25.933 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.333 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.064 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS 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 RECORD CONTAINS 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.PEG MOLECULE AND TRIS ANION FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.181
1054
5.1 %
RANDOM
Rwork
0.171
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obs
0.171
20606
99.85 %
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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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