+Open data
-Basic information
Entry | Database: PDB / ID: 1ks9 | ||||||
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Title | Ketopantoate Reductase from Escherichia coli | ||||||
Components | 2-DEHYDROPANTOATE 2-REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PanE / ApbA / KETOPANTOATE REDUCTASE / ROSSMANN FOLD / MONOMER / APO | ||||||
Function / homology | Function and homology information 2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Matak-Vinkovic, D. / Vinkovic, M. / Saldanha, S.A. / Ashurst, J.A. / von Delft, F. / Inoue, T. / Miguel, R.N. / Smith, A.G. / Blundell, T.L. / Abell, C. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structure of Escherichia coli ketopantoate reductase at 1.7 A resolution and insight into the enzyme mechanism. Authors: Matak-Vinkovic, D. / Vinkovic, M. / Saldanha, S.A. / Ashurst, J.L. / von Delft, F. / Inoue, T. / Miguel, R.N. / Smith, A.G. / Blundell, T.L. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ks9.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ks9.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ks9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ks9_validation.pdf.gz | 367.1 KB | Display | wwPDB validaton report |
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Full document | 1ks9_full_validation.pdf.gz | 376.1 KB | Display | |
Data in XML | 1ks9_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1ks9_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ks9 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ks9 | 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: 32479.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panE (apbA) / Plasmid: pET24b-panE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A9J4, 2-dehydropantoate 2-reductase |
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#2: 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: 2.31 Å3/Da / Density % sol: 46.69 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: PEG 4000, Tris, sodium acetate, pH 9.4, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 22, 1999 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 32249 / Num. obs: 32249 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.1 / % possible all: 74.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 5.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→30 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.788 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 30610 / σ(I): 0 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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