+Open data
-Basic information
Entry | Database: PDB / ID: 1y89 | ||||||
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Title | Crystal Structure of devB protein | ||||||
Components | devB protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / PSI / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt, oxidative branch / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar eltor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Lazarski, K. / Cymborowski, M. / Chruszcz, M. / Zheng, H. / Zhang, R. / Lezondra, L. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of devB protein Authors: Lazarski, K. / Cymborowski, M. / Chruszcz, M. / Zheng, H. / Zhang, R. / Lezondra, L. / Joachimiak, A. / Minor, W. | ||||||
History |
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Remark 600 | HETEROGEN the ligands labelled PE5 are fragments of PEG molecules |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y89.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y89.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 1y89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y89 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y89 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 238 / Label seq-ID: 1 - 238
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26064.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria) Species: Vibrio cholerae / Strain: O1 biovar eltor str. N16961 / Production host: Escherichia coli (E. coli) / References: GenBank: 9658331, UniProt: Q9KL51*PLUS |
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-Non-polymers , 5 types, 607 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | ChemComp-2PE / | #5: Chemical | ChemComp-PEG / | #6: 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: 3.68 Å3/Da / Density % sol: 66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 40% PEG-300, HEPES pH 7.5, 0.2 M NaCl, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 / Wavelength: 0.9794 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 26, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 52566 / Num. obs: 52566 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.55 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.44 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→41.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.619 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.964 Å2
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Refinement step | Cycle: LAST / Resolution: 2→41.42 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1802 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 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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