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Yorodumi- PDB-3kd8: Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kd8 | ||||||
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Title | Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728 | ||||||
Components | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase | ||||||
Keywords | ISOMERASE / phosphoglycerate mutase / structural genomics / PSI-2 / protein genomics / MCSG / glycolysis isomerase / Protein Structure Initiative / Midwest Center for Structural Genomics / Glycolysis | ||||||
Function / homology | Function and homology information phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glycolytic process / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Joachimiak, A. / Duke, N.E.C. / Marshall, N. / Buck, K. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728 Authors: Joachimiak, A. / Duke, N.E.C. / Marshall, N. / Buck, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kd8.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kd8.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kd8_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 3kd8_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 3kd8_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3kd8_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/3kd8 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kd8 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 43963.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: apgM, Ta0413 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Magic / References: UniProt: Q9HL27, EC: 5.4.2.1 #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: 46.49 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.16M magnesium chloride 0.08M tris HCl, pH 8.5 24% PEG 4000 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97880, 0.97904 | |||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 18, 2009 / Details: double-crystal monochromator Si(111) | |||||||||
Radiation | Monochromator: Silicon (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→73.92 Å / Num. obs: 25760 / % possible obs: 99.84 % / Observed criterion σ(F): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 30.75 | |||||||||
Reflection shell | Resolution: 2.6→2.62 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.923 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→73.92 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.677 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 1.18 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Authors state that residue B58 and B270 do not have well-defined side chain because of weak electron density at the region.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.771 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→73.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.665 Å / Total num. of bins used: 20
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