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Yorodumi- PDB-3h6e: The crystal structure of a carbohydrate kinase from Novosphingobi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h6e | ||||||
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Title | The crystal structure of a carbohydrate kinase from Novosphingobium aromaticivorans | ||||||
Components | Carbohydrate kinase, FGGY | ||||||
Keywords | TRANSFERASE / carbohydrate kinase / Novosphingobium aromaticivorans / strain DSM 12444 / SGX / 11200i / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information phosphotransferase activity, alcohol group as acceptor / kinase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of carbohydrate kinase from Novosphingobium aromaticivorans Authors: Zhang, Z. / 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 | 3h6e.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6e.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 3h6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6e ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6e | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53312.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: DSM 12444 / Gene: Saro_1051 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-codon+RIL - Stratagene / References: UniProt: Q2G9H7 #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: 2.3 Å3/Da / Density % sol: 46.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Magnesesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→114.71 Å / Num. obs: 35006 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 38.41 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 11.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→51.279 Å / SU ML: 0.37 / Isotropic thermal model: isotropic / σ(F): 1.14 / Phase error: 26.25 / 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 / Bsol: 36.755 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→51.279 Å
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Refine LS restraints |
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LS refinement shell |
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