- PDB-3hoi: Crystal structure of FMN-dependent nitroreductase BF3017 from Bac... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3hoi
Title
Crystal structure of FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 (YP_212631.1) from Bacteroides fragilis NCTC 9343 at 1.55 A resolution
Components
FMN-dependent nitroreductase BF3017
Keywords
OXIDOREDUCTASE / YP_212631.1 / FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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Components
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Protein , 1 types, 1 molecules A
#1: Protein
FMN-dependentnitroreductaseBF3017
Mass: 21329.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria) Gene: BF3017, YP_212631.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LB10
Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THE CONSTRUCT (RESIDUES 20-211) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-211) 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2000M Li2SO4, 20.0000% PEG-1000, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.55→29.514 Å / Num. obs: 31895 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 13.59 % / Biso Wilson estimate: 20.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.72
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
1.55-1.61
0.016
1.6
45676
1
98.6
1.61-1.67
0.016
2.2
40161
1
99.3
1.67-1.75
0.016
3
45319
1
99.2
1.75-1.84
0.016
4.5
41906
1
99.4
1.84-1.95
0.016
6.9
41720
1
99.4
1.95-2.1
0.016
10.9
43643
1
99.7
2.1-2.31
0.016
16.5
43972
1
99.8
2.31-2.65
0.016
23.2
44744
1
99.9
2.65-3.33
0.016
35.7
43272
1
99.9
3.33-29.5
0.016
51.5
42895
1
99.6
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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: 1.55→29.514 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 3.148 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074 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. FLAVIN MONONUCLEOTIDE COFACTOR (FMN) AND AN UNKNOWN LIGAND (UNL) ARE MODELED INTO THE PUTATIVE ACTIVE SITE. DURING THE REFINEMENT, THE FMN RESTRAINTS DICTIONARY WAS MODIFIED TO ALLOW BENDING OF THE ISOALLOXAZINE RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT BETWEEN THE FMN COORDINATES AND ELECTRON DENSITY. 5. SULFATE IONS (SO4), CITRATE ANION (FLC) FROM CRYSTALLIZATION SOLUTION, AND PEG1000 OR PEG200 FRAGMENTS (PEG) FROM EITHER CRYSTALLIZATION OR CRYO SOLUTION ARE MODELED. 6. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 185 WAS NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.187
1599
5 %
RANDOM
Rwork
0.161
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obs
0.162
31746
99.52 %
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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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