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Yorodumi- PDB-6i06: Crystal structure of psychrophilic phosphoglycerate kinase from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i06 | ||||||
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Title | Crystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18 | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | TRANSFERASE / hinge binding / kinase / glycolysis | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas (RNA similarity group I) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Mandelman, D. / Haser, R. / Aghajari, N. | ||||||
Funding support | France, 1items
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Citation | Journal: Extremophiles / Year: 2019 Title: Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase. Authors: Mandelman, D. / Ballut, L. / Wolff, D.A. / Feller, G. / Gerday, C. / Haser, R. / Aghajari, N. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2001 Title: Crystallization and preliminary X-ray analysis of a bacterial psychrophilic enzyme, phosphoglycerate kinase. Authors: Mandelman, D. / Bentahir, M. / Feller, G. / Gerday, C. / Haser, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i06.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i06.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i06_validation.pdf.gz | 414.9 KB | Display | wwPDB validaton report |
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Full document | 6i06_full_validation.pdf.gz | 416.2 KB | Display | |
Data in XML | 6i06_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 6i06_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i06 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i06 | HTTPS FTP |
-Related structure data
Related structure data | 6hxeSC 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: 40302.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: There is a mismatch between the sequence deposited in uniprot (ID: Q9RBS3) and the structure at position 150. This should clearly be a Ser as judged from the electron density and not a Pro ...Details: There is a mismatch between the sequence deposited in uniprot (ID: Q9RBS3) and the structure at position 150. This should clearly be a Ser as judged from the electron density and not a Pro as listed in the sequence. Idem for residue 219 which is not a Ser but an Asp, and residue 358 which is not a Tyr but a Gln. Following residues have been refined as alanines due to missing electron density for the side-chains: Q12, K102, K116 and the K248 has been refined as a Ser and Ser266 as a Gly due to missing electron density Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Gene: pgk / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RBS3, phosphoglycerate kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 10000 and 0.1 M HEPES at pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.90005 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90005 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.55 Å / Num. obs: 23306 / % possible obs: 99.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2→2.09 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6HXE Resolution: 2→29.55 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 55.0185 Å / Origin y: 6.3529 Å / Origin z: 0.4371 Å
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Refinement TLS group | Selection details: all |