+Open data
-Basic information
Entry | Database: PDB / ID: 1tk9 | ||||||
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Title | Crystal Structure of Phosphoheptose isomerase 1 | ||||||
Components | Phosphoheptose isomerase 1D-sedoheptulose 7-phosphate isomerase | ||||||
Keywords | ISOMERASE / Lipopolysaccharide biosynthesis / STRUCTURAL GENOMICS / NYSGXRC / T1512 / LPC1_CAMJE / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
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 | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Rajashankar, K.R. / Solorzano, V. / Kniewel, R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structures of two putative phosphoheptose isomerases. Authors: Seetharaman, J. / Rajashankar, K.R. / Solorzano, V. / Kniewel, R. / Lima, C.D. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tk9.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tk9.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tk9 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tk9 | 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: 20546.020 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: LPCA1, GMHA1, CJ1149C / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: Q9PNE6, Isomerases #2: 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: 2.42 Å3/Da / Density % sol: 48.8 % / Description: Structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% peg mme 2k, 0.1M bis-tris, 0.1M na acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 30, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 93549 / Num. obs: 93549 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.07 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.075 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.94 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 9243 / Rsym value: 0.408 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: Experimental electron density Resolution: 2.1→19.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 213473.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.5165 Å2 / ksol: 0.322302 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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