+Open data
-Basic information
Entry | Database: PDB / ID: 1rp7 | ||||||
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Title | E. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX | ||||||
Components | Pyruvate dehydrogenase E1 component | ||||||
Keywords | OXIDOREDUCTASE / THDP / THIAMIN-THIAZOLONE DIPHOSPHATE / PYRUVATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information : / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity ...: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / membrane / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.09 Å | ||||||
Authors | Arjunan, P. / Chandrasekhar, K. / Furey, W. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural Determinants of Enzyme Binding Affinity: The E1 Component of Pyruvate Dehydrogenase from Escherichia coli in Complex with the Inhibitor Thiamin Thiazolone Diphosphate. Authors: Arjunan, P. / Chandrasekhar, K. / Sax, M. / Brunskill, A. / Nemeria, N. / Jordan, F. / Furey, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rp7.cif.gz | 336.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rp7.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/1rp7 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/1rp7 | HTTPS FTP |
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-Related structure data
Related structure data | 1l8aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 99657.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli, Escherichia coli O157:H7 Genus: Escherichia, Escherichia / Species: , Escherichia coli / Strain: , O157:H7 / Gene: ACEE, B0114, Z0124, ECS0118 / Plasmid: JRG PGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456 References: UniProt: P06958, UniProt: P0AFG8*PLUS, pyruvate dehydrogenase (acetyl-transferring) #2: Chemical | #3: Chemical | #4: 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: 2.33 Å3/Da / Density % sol: 47.12 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.05 Details: PEG2000 MONOMETHYL ETHER, PROPANOL,SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, THIAMIN-THIAZOLONE DIPHOSPHATE, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072 / Wavelength: 1.072 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jan 27, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: CURVED SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→40.6 Å / Num. all: 107597 / Num. obs: 100232 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 2.09→2.15 Å / Redundancy: 1.23 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.84 / Num. unique all: 8714 / Rsym value: 0.203 / % possible all: 55.1 |
Reflection | *PLUS Highest resolution: 2.09 Å / Num. measured all: 351214 |
Reflection shell | *PLUS % possible obs: 55.1 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1L8A Resolution: 2.09→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.2 Å / Total num. of bins used: 7
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Refinement | *PLUS Num. reflection obs: 85348 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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