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Yorodumi- PDB-1lk7: Structure of D-Ribose-5-Phosphate Isomerase from in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lk7 | ||||||
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Title | Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid | ||||||
Components | D-Ribose-5-Phosphate Isomerase | ||||||
Keywords | ISOMERASE / alpha/beta structure | ||||||
Function / homology | Function and homology information ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ishikawa, K. / Matsui, I. / Payan, F. / Cambillau, C. / Ishida, H. / Kawarabayasi, Y. / Kikuchi, H. / Roussel, A. | ||||||
Citation | Journal: STRUCTURE / Year: 2002 Title: A Hyperthermostable D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii Characterization and Three-Dimensional Structure Authors: Ishikawa, K. / Matsui, I. / Payan, F. / Cambillau, C. / Ishida, H. / Kawarabayasi, Y. / Kikuchi, H. / Roussel, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lk7.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lk7.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lk7 ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lk7 | HTTPS FTP |
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-Related structure data
Related structure data | 1lk5SC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is the tetramer in the asymetric unit |
-Components
#1: Protein | Mass: 25189.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50083, ribose-5-phosphate isomerase #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-DER / #5: 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: 2.51 Å3/Da / Density % sol: 51.03 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M acetate buffer, 2.0M NaCl, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. all: 70244 / Num. obs: 67418 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 96.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 96.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LK5 Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with REFMAC
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å
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Refinement | *PLUS Num. reflection obs: 65509 / Num. reflection Rfree: 3322 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.239 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.25 |