- PDB-3er7: Crystal structure of NTF2-like protein of unknown function (YP_00... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3er7
Title
Crystal structure of NTF2-like protein of unknown function (YP_001812677.1) from EXIGUOBACTERIUM SP. 255-15 at 1.50 A resolution
Components
uncharacterized NTF2-like protein
Keywords
structural genomics / unknown function / YP_001812677.1 / 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 / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Function and homology information
Biological species
Exiguobacterium sibiricum 255-15 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS FORMING A DIMER. CRYSTAL PACKING ANALYSIS SUGGESTS THAT THIS IS THE OLIGOMERIC FORM IN SOLUTION.
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Components
#1: Protein
uncharacterizedNTF2-likeprotein
Mass: 15092.669 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium sibiricum 255-15 (bacteria) Gene: YP_001812677.1, Exig_0174 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B1YHC8
Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.5→29.514 Å / Num. obs: 40169 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.153 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.44
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
1.55-1.61
0.425
1.9
13589
7230
97
1.61-1.67
0.321
2.4
11954
6320
99.6
1.67-1.75
0.254
3.1
13587
7175
99.3
1.75-1.84
0.174
4.4
12510
6583
99.2
1.84-1.95
0.105
7.2
12569
6574
99.1
1.95-2.1
0.068
10.6
13056
6811
99.1
2.1-2.31
0.047
14.6
13114
6820
98.8
2.31-2.65
0.037
18.4
13458
6975
99.2
2.65-3.33
0.024
26.7
13140
6776
99
3.33
0.019
34.9
13402
6859
98.2
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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
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.5→29.514 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.82 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 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.CHLORIDE AND PEG (PEG3000 FRAGMENTS) FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.IT APPEARS PLAUSIBLE THAT A DISULFIDE BOND MAY FORM BETWEEN CYS87 RESIDUES IN CHAINS A AND B.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.209
2014
5 %
RANDOM
Rwork
0.176
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obs
0.178
40122
99.68 %
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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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