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Yorodumi- PDB-5kgm: 2.95A resolution structure of Apo independent phosphoglycerate mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kgm | ||||||
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Title | 2.95A resolution structure of Apo independent phosphoglycerate mutase from C. elegans (monoclinic form) | ||||||
Components | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase | ||||||
Keywords | ISOMERASE / metal binding / coupled enzyme assay / HTS / structure activity relationship / RaPID systems / high throughput enzymology | ||||||
Function / homology | Function and homology information phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glucose catabolic process / glycolytic process / manganese ion binding / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | ||||||
Authors | Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Yu, H. / Dranchak, P. / MacArthur, R. / Li, Z. / Carlow, T. / Suga, H. / Inglese, J. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Authors: Yu, H. / Dranchak, P. / Li, Z. / MacArthur, R. / Munson, M.S. / Mehzabeen, N. / Baird, N.J. / Battalie, K.P. / Ross, D. / Lovell, S. / Carlow, C.K. / Suga, H. / Inglese, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kgm.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kgm.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kgm_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 5kgm_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 5kgm_validation.xml.gz | 34 KB | Display | |
Data in CIF | 5kgm_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/5kgm ftp://data.pdbj.org/pub/pdb/validation_reports/kg/5kgm | HTTPS FTP |
-Related structure data
Related structure data | 5kglC 5kgnC 1o98S C: citing same article (ref.) S: Starting model for refinement |
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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: 60823.000 Da / Num. of mol.: 2 / Fragment: isoform a Source method: isolated from a genetically manipulated source Details: Full length (M1 to I539, isoform a) / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ipgm-1, F57B10.3 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C2566/T7 Express References: UniProt: G5EFZ1, phosphoglycerate mutase (2,3-diphosphoglycerate-independent) #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | |
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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: 2.67 Å3/Da / Density % sol: 53.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% (w/v) PEG 5000 MME, 0.1 M MES , 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.95→46.48 Å / Num. obs: 27020 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.55 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.09 / Rrim(I) all: 0.168 / Net I/σ(I): 9 / Num. measured all: 90718 / Scaling rejects: 4 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O98 Resolution: 2.95→42.982 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 25.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.94 Å2 / Biso mean: 48.5937 Å2 / Biso min: 18.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→42.982 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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