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Yorodumi- PDB-1x77: Crystal structure of a NAD(P)H-dependent FMN reductase complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x77 | ||||||
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Title | Crystal structure of a NAD(P)H-dependent FMN reductase complexed with FMN | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative (PSI) / FMN reductase / FMN bound / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information FMN reductase (NADPH) activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Agarwal, R. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal. Authors: Agarwal, R. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x77.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x77.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 1x77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/1x77 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/1x77 | HTTPS FTP |
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-Related structure data
Related structure data | 1rttSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21118.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4D4 #2: Chemical | #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: 2.9 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, Calcium acetate, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2004 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. all: 13038 / Num. obs: 13038 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.69→2.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Num. unique all: 1349 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RTT Resolution: 2.7→44.89 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 377503.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The electron density was weak or absent for the missing residues.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.7536 Å2 / ksol: 0.332809 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 41 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→44.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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