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- PDB-1rpx: D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE FROM SOLANUM TUBEROSUM CHLOROPLASTS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rpx | ||||||
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Title | D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE FROM SOLANUM TUBEROSUM CHLOROPLASTS | ||||||
![]() | PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE) | ||||||
![]() | 3-EPIMERASE / CHLOROPLAST / CALVIN CYCLE / OXIDATIVE PENTOSE PHOSPHATE PATHWAY | ||||||
Function / homology | ![]() : / ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / pentose catabolic process / pentose-phosphate shunt, non-oxidative branch / reductive pentose-phosphate cycle / chloroplast thylakoid membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kopp, J. / Schulz, G.E. | ||||||
![]() | ![]() Title: Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. Authors: Kopp, J. / Kopriva, S. / Suss, K.H. / Schulz, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.4 KB | Display | ![]() |
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PDB format | ![]() | 112.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.1 KB | Display | ![]() |
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Full document | ![]() | 458.1 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 24644.363 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 67 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1996 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. obs: 49783 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 33.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.206 / % possible all: 87.1 |
Reflection | *PLUS Num. measured all: 265449 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 87.1 % / Rmerge(I) obs: 0.206 |
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Processing
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Refinement | Method to determine structure: ![]() Details: STANDARD BULK SOLVENT CORRECTION OF X-PLOR 3.851 USED
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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