+Open data
-Basic information
Entry | Database: PDB / ID: 1x94 | ||||||
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Title | Crystal Structure of a Hypothetical protein | ||||||
Components | putative Phosphoheptose isomeraseD-sedoheptulose 7-phosphate isomerase | ||||||
Keywords | ISOMERASE / Hypothetical protein / Vibrio cholerae / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
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 / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Seetharaman, J. / Swaminathan, S. / 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 | 1x94.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x94.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1x94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x94 ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x94 | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 20673.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lpcA, gmhA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KPY2 #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: 2.4 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Ammonium Acetate, Bis Tris, NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97862,0.97904,0.94 | ||||||||||||
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Mar 4, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 18477 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.3 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.55 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→44.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 206203.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: the electron density was absent or weak for the missing residues.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9903 Å2 / ksol: 0.385244 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→44.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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