+Open data
-Basic information
Entry | Database: PDB / ID: 1d8w | ||||||
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Title | L-RHAMNOSE ISOMERASE | ||||||
Components | L-RHAMNOSE ISOMERASE | ||||||
Keywords | ISOMERASE / BETA-ALPHA-8-BARRELS / ALDOSE-KETOSE ISOMERIZATION / HYDRIDE SHIFT | ||||||
Function / homology | Function and homology information L-rhamnose isomerase / rhamnose binding / L-lyxose metabolic process / L-rhamnose isomerase activity / rhamnose catabolic process / manganese ion binding / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Korndorfer, I.P. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. Authors: Korndorfer, I.P. / Fessner, W.D. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d8w.cif.gz | 365.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d8w.ent.gz | 296.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d8w ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d8w | HTTPS FTP |
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-Related 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: 48592.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28(B)+ FROM NEW ENGLAND BIOLABS / Production host: Escherichia coli (E. coli) / References: UniProt: P32170, L-rhamnose isomerase #2: Chemical | ChemComp-ZN / #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: 2.61 Å3/Da / Density % sol: 52.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.2 M CITRATE, 22.5-30% PEG 8000, 10% ISOPROPANOLE, 0.1 M HEPES, PH = 6.4 - 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 491294 / Num. obs: 426996 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 1.68 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.33 / % possible all: 84.4 |
Reflection | *PLUS Num. obs: 252886 / % possible obs: 96 % / Num. measured all: 426996 |
Reflection shell | *PLUS % possible obs: 84 % |
-Processing
Software |
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Refinement | Resolution: 1.6→30 Å / Stereochemistry target values: TRONRUD TNT / Details: CONJUGATE DIRECTIONS MINIMIZATION, NO NCS
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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