- PDB-3g14: Crystal structure of nitroreductase family protein (YP_877874.1) ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3g14
Title
Crystal structure of nitroreductase family protein (YP_877874.1) from Clostridium novyi NT at 1.75 A resolution
Components
Nitroreductase family protein
Keywords
OXIDOREDUCTASE / YP_877874.1 / nitroreductase family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Mass: 18.015 Da / Num. of mol.: 275 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97876
1
3
0.97826
1
Reflection
Resolution: 1.75→28.194 Å / Num. obs: 34941 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.426 Å2 / Rmerge(I) obs: 0.056
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.75-1.81
0.499
1.4
9468
5956
1
90.2
1.81-1.89
0.346
2
11911
7511
1
98.6
1.89-1.97
0.235
2.9
10013
6279
1
98.8
1.97-2.07
0.189
3.7
10432
6527
1
98.6
2.07-2.2
0.124
5.4
10967
6846
1
98.6
2.2-2.37
0.095
7
11049
6865
1
98.4
2.37-2.61
0.067
9.3
11008
6817
1
98.3
2.61-2.99
0.049
12.2
11041
6775
1
97.9
2.99-3.76
0.034
17
10889
6648
1
96.9
3.76-28.194
0.026
22.2
10969
6625
1
95.4
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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
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.75→28.194 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.021 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.12 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. SULFATE (SO4), ACETATE (ACT) IONS AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION CONDITION WERE MODELED. 5. RESIDUES 156-164 OF A CHAIN AND 157-163 OF B CHAIN WERE NOT VISIBLE IN THE ELECTRON DENSITIES. THEY WERE UNMODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.219
1754
5 %
RANDOM
Rwork
0.173
-
-
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obs
0.176
34929
99.35 %
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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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