[English] 日本語
Yorodumi- PDB-1flm: DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1flm | ||||||
---|---|---|---|---|---|---|---|
Title | DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) | ||||||
Components | PROTEIN (FMN-BINDING PROTEIN) | ||||||
Keywords | ELECTRON TRANSPORT / FMN BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.3 Å | ||||||
Authors | Suto, K. / Kawagoe, K. / Shibata, N. / Morimoto, K. / Higuchi, Y. / Kitamura, M. / Nakaya, T. / Yasuoka, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: How do the x-ray structure and the NMR structure of FMN-binding protein differ? Authors: Suto, K. / Kawagoe, K. / Shibata, N. / Morimoto, Y. / Higuchi, Y. / Kitamura, M. / Nakaya, T. / Yasuoka, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1flm.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1flm.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 1flm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1flm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1flm_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1flm_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1flm_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1flm ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1flm | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99999, 0.00427, 0.00202), Vector: |
-Components
#1: Protein | Mass: 13153.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / Cellular location: CYTOPLASM / Plasmid: PMKBT-100 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q46604 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 49.89 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: 20% PEG6000, 0.1M TRIS(PH7.5), 20% GRYCEROL, 0.2M NACL | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 68514 / % possible obs: 86.6 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 2 / % possible all: 60.6 |
Reflection | *PLUS Num. measured all: 337547 / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS % possible obs: 60.6 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|