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Yorodumi- PDB-3vnm: Crystal structures of D-Psicose 3-epimerase with D-sorbose from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vnm | ||||||
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Title | Crystal structures of D-Psicose 3-epimerase with D-sorbose from Clostridium cellulolyticum H10 | ||||||
Components | Xylose isomerase domain protein TIM barrel | ||||||
Keywords | ISOMERASE / D-Psicose 3-epimerase / Clostridium cellulolyticum H10 / ketohexose / TIM barrel | ||||||
Function / homology | Function and homology information D-psicose 3-epimerase / racemase and epimerase activity, acting on carbohydrates and derivatives / cobalt ion binding / manganese ion binding Similarity search - Function | ||||||
Biological species | Clostridium cellulolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Chan, H.C. / Zhu, Y. / Hu, Y. / Ko, T.P. / Huang, C.H. / Ren, F. / Chen, C.C. / Guo, R.T. / Sun, Y. | ||||||
Citation | Journal: Protein Cell / Year: 2012 Title: Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars. Authors: Chan, H.C. / Zhu, Y. / Hu, Y. / Ko, T.P. / Huang, C.H. / Ren, F. / Chen, C.C. / Ma, Y. / Guo, R.T. / Sun, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vnm.cif.gz | 249.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vnm.ent.gz | 200.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vnm_validation.pdf.gz | 475.9 KB | Display | wwPDB validaton report |
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Full document | 3vnm_full_validation.pdf.gz | 498.2 KB | Display | |
Data in XML | 3vnm_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 3vnm_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vnm ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vnm | HTTPS FTP |
-Related structure data
Related structure data | 3vniSC 3vnjC 3vnkC 3vnlC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 33076.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Strain: H10 / Gene: Ccel_0941 / Plasmid: pET-21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8I944 #2: Sugar | ChemComp-SDD / #3: Chemical | ChemComp-MN / #4: 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: 3.07 Å3/Da / Density % sol: 59.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.2M tri-sodium citrate dehydrate, 17-20% Polyethylene Glycol 3350, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.12→25 Å / Num. obs: 90274 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.053 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 8993 / Rsym value: 0.496 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VNI Resolution: 2.12→25 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.12→25 Å
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