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Yorodumi- PDB-3klb: Crystal structure of Putative Flavoprotein in Complex with FMN (Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3klb | ||||||
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Title | Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution | ||||||
Components | Putative Flavoprotein | ||||||
Keywords | FLAVOPROTEIN / Putative Flavoprotein in Complex with FMN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides fragilis NCTC 9343 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3klb.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3klb.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 3klb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3klb_validation.pdf.gz | 763.3 KB | Display | wwPDB validaton report |
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Full document | 3klb_full_validation.pdf.gz | 764.9 KB | Display | |
Data in XML | 3klb_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3klb_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3klb ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klb | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18298.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria) Strain: ATCC 25285 / NCTC 9343 / Gene: BF4115 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5L808 |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | ChemComp-FMN / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE CONSTRUCT (1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-161) WAS EXPRESSED WITH A PURIFICATI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10.0000% Glycerol, 1.2600M sodium citrate, 0.1M HEPES pH 7.5, Additive: 0.001 M FMN, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97939,0.97927 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2009 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→27.832 Å / Num. obs: 23388 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.346 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.33 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→27.832 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.281 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087 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 ...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). A MODIFIED FMN RESTRAINTS DICTIONARY WAS USED DURING THE REFINEMENT TO ALLOW BENDING OF THE FMN RING ALONG THE N5-N10 VIRTUAL AXIS. THIS RESULTS IN AN IMPROVED FIT BETWEEN THE FMN COORDINATE MODEL AND ELECTRON DENSITY. (5). SODIUM ION (NA) AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELED.
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.13 Å2 / Biso mean: 29.843 Å2 / Biso min: 15.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→27.832 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.752→1.798 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 31.3526 Å / Origin y: 10.2525 Å / Origin z: 29.4288 Å
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