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Yorodumi- PDB-1dv2: The structure of biotin carboxylase, mutant E288K, complexed with ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dv2 | ||||||
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Title | The structure of biotin carboxylase, mutant E288K, complexed with ATP | ||||||
Components | BIOTIN CARBOXYLASE | ||||||
Keywords | LIGASE / ATP-grasp biotin-dependent carboxylase | ||||||
Function / homology | Function and homology information biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding ...biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Thoden, J.B. / Blanchard, C.Z. / Holden, H.M. / Waldrop, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Movement of the biotin carboxylase B-domain as a result of ATP binding. Authors: Thoden, J.B. / Blanchard, C.Z. / Holden, H.M. / Waldrop, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dv2.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dv2.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dv2 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dv2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49668.996 Da / Num. of mol.: 2 / Fragment: BIOTIN CARBOXYLASE / Mutation: E288K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P24182, biotin carboxylase #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: 2.89 Å3/Da / Density % sol: 57.46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG-8000 ATP magnesium chloride HEPPS potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 37574 / Num. obs: 37574 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.297 / Num. unique all: 3543 / % possible all: 73.1 |
Reflection | *PLUS Num. measured all: 82537 |
Reflection shell | *PLUS % possible obs: 73.1 % / Num. unique obs: 3543 / Num. measured obs: 4686 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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