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Yorodumi- PDB-3gbh: CRYSTAL STRUCTURE OF A PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE (SE196... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gbh | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE (SE1966) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 2.00 A RESOLUTION | ||||||
Components | NAD(P)H-flavin oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus epidermidis ATCC 12228 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_765521.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 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 | 3gbh.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gbh.ent.gz | 162.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gbh ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gbh | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24775.629 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis ATCC 12228 (bacteria) Gene: NP_765521.1, SE_1966 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8CN78, UniProt: A0A0H2VHN8*PLUS |
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-Non-polymers , 6 types, 582 molecules
#2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-CA / #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: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: NANODROP, 30.0% PEG 200, 5.0% PEG 3000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97968 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97968 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→29.514 Å / Num. obs: 58789 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.417 Å2 / Rmerge(I) obs: 0.117 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 2→29.514 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.097 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.139 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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. FLAVIN MONONUCLEOTIDE COFACTOR (FMN) AND AN UNKNOWN LIGAND (UNL) ARE MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH MONOMER. 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. GLYCEROL MOLECULES (GOL) FROM THE CRYOPROTECTANT ARE MODELED INTO THE STRUCTURE. 6. SEVERAL ELECTRON DENSITY PEAKS BETWEEN SYMMETRY-RELATED SUBUNITS WERE OBSERVED ADJACENT TO GLUTAMIC AND ASPARTIC ACID SIDECHAINS, AND THE MAGNITUDE OF THESE DENSITY PEAKS IS CONSISTENT WITH THE X-RAY SCATTERING FROM A CALCIUM ATOM. THEREFORE, SEVERAL CALCIUM ATOMS WERE MODELED INTO THE STRUCTURE.
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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: 62.46 Å2 / Biso mean: 26.721 Å2 / Biso min: 11.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.514 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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