+Open data
-Basic information
Entry | Database: PDB / ID: 1ri6 | ||||||
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Title | Structure of a putative isomerase from E. coli | ||||||
Components | putative isomerase ybhE | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ISOMERASE / 7-BLADED PROPELLER / ENZYME / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information 6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / glucose metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å | ||||||
Authors | Lima, C.D. / Kniewel, R. / Solorzano, V. / Wu, J. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Structure of a putative 7-bladed propeller isomerase Authors: Lima, C.D. / Kniewel, R. / Solorzano, V. / Wu, J. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. THE AUTHORS STATE IT MAY BE A MONOMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ri6.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ri6.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ri6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1ri6 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1ri6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | UNKNOWN, POSSIBLE MONOMER |
-Components
#1: Protein | Mass: 37719.949 Da / Num. of mol.: 1 / Mutation: P84L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBHE / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P52697 |
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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: 2.1 Å3/Da / Density % sol: 41.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 17.5% PEG 4k 0.1M Na Cacodylate 6.5 5% Ethylene Glycol , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2003 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 22379 / Num. obs: 22289 / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2→19.62 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1735786.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.9204 Å2 / ksol: 0.359933 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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