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Yorodumi- PDB-4dib: The crystal structure of glyceraldehyde-3-phosphate dehydrogenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dib | ||||||
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Title | The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne | ||||||
Components | Glyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NIAID / structural genomics / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Rossmann fold / CSGID | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glucose metabolic process / NAD binding / NADP binding / protease binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Nocek, B. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne Authors: Nocek, B. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dib.cif.gz | 475 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dib.ent.gz | 388.2 KB | Display | PDB format |
PDBx/mmJSON format | 4dib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dib_validation.pdf.gz | 522.9 KB | Display | wwPDB validaton report |
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Full document | 4dib_full_validation.pdf.gz | 615.1 KB | Display | |
Data in XML | 4dib_validation.xml.gz | 97.5 KB | Display | |
Data in CIF | 4dib_validation.cif.gz | 132.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/4dib ftp://data.pdbj.org/pub/pdb/validation_reports/di/4dib | HTTPS FTP |
-Related structure data
Related structure data | 3cmcS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 37829.246 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: gap1, BA_4827, BAS4478, GBAA_4827 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) References: UniProt: Q81L07, UniProt: A0A348AAL1*PLUS, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: 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: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M lithium sulfate, 25.5% PEG3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→40 Å / Num. all: 90350 / Num. obs: 87718 / % possible obs: 97.2 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 2.1 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.55→2.59 Å / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CMC Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.861 / SU B: 12 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 26.473 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.596 Å / Total num. of bins used: 20
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