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Yorodumi- PDB-5by2: Sedoheptulose 7-phosphate isomerase from Colwellia psychrerythrae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5by2 | ||||||
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Title | Sedoheptulose 7-phosphate isomerase from Colwellia psychrerythraea strain 34H | ||||||
Components | Phosphoheptose isomerase | ||||||
Keywords | ISOMERASE / CpsGmhA / Sedoheptulose 7-phosphate isomerase / Psychrophile / Colwellia psychrerythraea strain 34H | ||||||
Function / homology | Function and homology information D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / carbohydrate derivative binding / carbohydrate metabolic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Colwellia psychrerythraea 34H (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Lee, J.H. / Chang, J.H. / Do, H. / Yun, J.S. | ||||||
Citation | Journal: Mol.Cells / Year: 2015 Title: Crystal Structure and Comparative Sequence Analysis of GmhA from Colwellia psychrerythraea Strain 34H Provides Insight into Functional Similarity with DiaA Authors: Do, H. / Yun, J.S. / Lee, C.W. / Choi, Y.J. / Kim, H.Y. / Kim, Y.J. / Park, H. / Chang, J.H. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5by2.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5by2.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 5by2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5by2_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 5by2_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 5by2_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5by2_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5by2 ftp://data.pdbj.org/pub/pdb/validation_reports/by/5by2 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21221.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea 34H (bacteria) Strain: 34H / Gene: gmhA, CPS_4434 / Production host: Escherichia coli (E. coli) References: UniProt: Q47VU0, D-sedoheptulose-7-phosphate isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 19%(v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44.28 Å / Num. obs: 4651 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 7.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.8→44.28 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 29.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.28 Å
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Refine LS restraints |
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LS refinement shell |
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