+Open data
-Basic information
Entry | Database: PDB / ID: 1nox | ||||||
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Title | NADH OXIDASE FROM THERMUS THERMOPHILUS | ||||||
Components | NADH OXIDASE | ||||||
Keywords | FLAVOENZYME / FLAVOPROTEIN FMN / OXIDOREDUCTASE / THERMOPHILE | ||||||
Function / homology | Function and homology information NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase (ubiquinone) activity Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS, MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Hecht, H.J. / Erdmann, H. / Park, H.J. / Sprinzl, M. / Schmid, R.D. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal structure of NADH oxidase from Thermus thermophilus. Authors: Hecht, H.J. / Erdmann, H. / Park, H.J. / Sprinzl, M. / Schmid, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nox.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nox.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nox_validation.pdf.gz | 784 KB | Display | wwPDB validaton report |
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Full document | 1nox_full_validation.pdf.gz | 789.8 KB | Display | |
Data in XML | 1nox_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1nox_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1nox ftp://data.pdbj.org/pub/pdb/validation_reports/no/1nox | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22780.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PTNADOX / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q60049, NADH dehydrogenase |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 0.05 M MES-TRIS BUFFER PH 6.0, 26 % PEG 4000, 0.3 M NACL, 50 MM FMN | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 6.6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.59 Å / Num. obs: 28064 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.069 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.071 / % possible all: 95.3 |
Reflection shell | *PLUS % possible obs: 95.3 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS, MOLECULAR REPLACEMENT Starting model: MODEL FROM ISOMORPHOUS REPLACEMENT Resolution: 1.59→21 Å / σ(F): 0 / Details: FREE-R-VALUE INTRODUCED LATE IN REFINEMENT.
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Displacement parameters | Biso mean: 23.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→21 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |