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Yorodumi- PDB-2ifa: Crystal Structure of the PUTATIVE NITROREDUCTASE (SMU.260) IN COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ifa | |||||||||
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Title | Crystal Structure of the PUTATIVE NITROREDUCTASE (SMU.260) IN COMPLEX WITH FMN FROM STREPTOCOCCUS MUTANS, NORTHEAST STRUCTURAL GENOMICS TARGET SMR5. | |||||||||
Components | Hypothetical protein SMU.260Hypothesis | |||||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptococcus mutans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | |||||||||
Authors | Forouhar, F. / Chen, Y. / Xiao, R. / Ma, L.C. / Byler, T. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ifa.cif.gz | 253.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ifa.ent.gz | 214.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ifa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/2ifa ftp://data.pdbj.org/pub/pdb/validation_reports/if/2ifa | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23662.988 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.260 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8DW21 #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 MM SODIUM ACETATE, 18% PEG3350, 240 MM AMMONIUM DIHYDROGEN PHOSPHATE, 10 MM FMN, AND 5 DTT., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97894 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.03 Å / Num. all: 110600 / Num. obs: 106951 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.057 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.2 / Num. unique all: 10679 / Rsym value: 0.203 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→29.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 244508.83 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.4646 Å2 / ksol: 0.328468 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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