- PDB-3hzp: Crystal structure of NTF2-like protein of unknown function MN2A_0... -
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Basic information
Entry
Database: PDB / ID: 3hzp
Title
Crystal structure of NTF2-like protein of unknown function MN2A_0505 from Prochlorococcus marinus (YP_291699.1) from Prochlorococcus sp. NATL2A at 1.40 A resolution
Components
NTF2-like protein of unknown function
Keywords
Structural Genomics / unknown function / YP_291699.1 / NTF2-like protein of unknown function MN2A_0505 from Prochlorococcus marinus / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Protein of unknown function DUF3804 / Protein of unknown function (DUF3804) / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Prochlorococcus marinus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 40.0000% PEG-600, 0.1M Citrate pH 5.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.4→29.025 Å / Num. obs: 24917 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 14.99 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 6.295
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
1.4-1.44
5.4
0.748
1
9847
1818
0.748
100
1.44-1.48
5.4
0.597
1.3
9606
1778
0.597
100
1.48-1.52
5.4
0.451
1.7
9317
1718
0.451
100
1.52-1.57
5.4
0.383
2
9108
1673
0.383
100
1.57-1.62
5.5
0.315
2.4
8715
1599
0.315
100
1.62-1.67
5.4
0.253
3
8687
1598
0.253
100
1.67-1.74
5.4
0.21
3.6
8238
1512
0.21
100
1.74-1.81
5.5
0.174
4.3
7915
1450
0.174
100
1.81-1.89
5.4
0.133
5.6
7775
1428
0.133
100
1.89-1.98
5.4
0.103
7.1
7307
1344
0.103
100
1.98-2.09
5.4
0.089
7.7
6985
1288
0.089
100
2.09-2.21
5.4
0.085
7.9
6625
1224
0.085
100
2.21-2.37
5.4
0.078
8.5
6098
1128
0.078
100
2.37-2.56
5.4
0.067
9.6
5911
1091
0.067
100
2.56-2.8
5.4
0.06
10.5
5430
1005
0.06
100
2.8-3.13
5.4
0.056
11.4
4816
893
0.056
100
3.13-3.61
5.4
0.057
11.1
4361
811
0.057
100
3.61-4.43
5.3
0.044
13.6
3635
687
0.044
100
4.43-6.26
5.1
0.039
16.2
2825
551
0.039
100
6.26-29.02
4.6
0.045
14.2
1473
321
0.045
98.5
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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
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.4→29.025 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.111 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.06 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(1PE) FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.184
1266
5.1 %
RANDOM
Rwork
0.167
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obs
0.168
24887
99.98 %
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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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