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Yorodumi- PDB-3e4v: Crystal structure of NADH:FMN oxidoreductase like protein in comp... -
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-Basic information
Entry | Database: PDB / ID: 3e4v | ||||||
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Title | Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 A resolution | ||||||
Components | NADH:FMN oxidoreductase like protein | ||||||
Keywords | FLAVOPROTEIN / YP_544701.1 / NADH:FMN oxidoreductase like protein in complex with FMN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methylobacillus flagellatus KT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 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 | 3e4v.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e4v.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 3e4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/3e4v ftp://data.pdbj.org/pub/pdb/validation_reports/e4/3e4v | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASN / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 3 - 181 / Label seq-ID: 4 - 182
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21175.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria) Gene: YP_544701.1, Mfla_0590 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1H3S7 |
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-Non-polymers , 6 types, 383 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 1.92 Å3/Da / Density % sol: 35.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M calcium acetate, 30.0% polyethylene glycol 400, 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2008 Details: 1m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→29.683 Å / Num. obs: 64048 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.374 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.74 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→29.683 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.689 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.051 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). 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. (3). FLAVIN MONONUCLEOTIDE (FMN) MOLECULES WERE COCRYSTALLIZED AND THE ELECTRON DENSITIES OF FMN WERE CONCLUSIVE. (4). SODIUM (NA) AND ACETATE (ACT) IONS, AND PEG 400 FRAGMENTS (PEG) FROM CRYSTALLIZATION CONDITIONS WERE 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.998 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.683 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2381 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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