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Yorodumi- PDB-2i22: Crystal structure of Escherichia coli phosphoheptose isomerase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i22 | ||||||
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Title | Crystal structure of Escherichia coli phosphoheptose isomerase in complex with reaction substrate sedoheptulose 7-phosphate | ||||||
Components | Phosphoheptose isomerase | ||||||
Keywords | ISOMERASE / lipopolysaccharide biosynthesis / phosphoheptose isomerase | ||||||
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 / lipopolysaccharide core region biosynthetic process / carbohydrate derivative binding / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Blakely, K. / Zhang, K. / DeLeon, G. / Wright, G. / Junop, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure and Function of Sedoheptulose-7-phosphate Isomerase, a Critical Enzyme for Lipopolysaccharide Biosynthesis and a Target for Antibiotic Adjuvants Authors: Taylor, P.L. / Blakely, K.M. / de Leon, G.P. / Walker, J.R. / McArthur, F. / Evdokimova, E. / Zhang, K. / Valvano, M.A. / Wright, G.D. / Junop, M.S. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS' ANALYTICAL ULTRACENTRIFUGATION AND GEL FILTRATION EXPERIMENTS SHOW THAT THE BIOLOGICAL ASSEMBLY IS A DIMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i22.cif.gz | 153.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i22.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 2i22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i22_validation.pdf.gz | 850.2 KB | Display | wwPDB validaton report |
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Full document | 2i22_full_validation.pdf.gz | 896.6 KB | Display | |
Data in XML | 2i22_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 2i22_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/2i22 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/2i22 | HTTPS FTP |
-Related structure data
Related structure data | 1x92C 2i2wC 3bjzC 1tk9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 192 / Label seq-ID: 21 - 212
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Details | The biological assembly is a dimer generated from either the A and D or B and C monomers within the asymmetric unit. |
-Components
#1: Protein | Mass: 23014.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gmhA, lpcA, tfrA, b0222 / Plasmid: pDEST17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P63224, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds #2: Chemical | ChemComp-I22 / | #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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 3% PEG 8000, 0.002 M DTT, 3% 1,6-hexanediol, 0.01 M Hepes, 0.1 M imidazole, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2005 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→47.39 Å / Num. all: 20533 / Num. obs: 20533 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.79→2.89 Å / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TK9 Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.346 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.337 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1357 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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