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Yorodumi- PDB-6hxe: Crystal structure of psychrophilic phosphoglycerate kinase from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hxe | ||||||
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Title | Crystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18 in complex with 3-phosphoglycerate | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | TRANSFERASE / Complex / 3-phosphoglycerate / hinge binding | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas sp. 'TAC II 18' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 6hxe.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hxe.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hxe_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 6hxe_full_validation.pdf.gz | 424 KB | Display | |
Data in XML | 6hxe_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 6hxe_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/6hxe ftp://data.pdbj.org/pub/pdb/validation_reports/hx/6hxe | HTTPS FTP |
-Related structure data
Related structure data | 6i06C 1vpeS 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: 40267.207 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: 27, 102, 243, 248, 268, 292, 327, 348 Source: (gene. exp.) Pseudomonas sp. 'TAC II 18' (bacteria) / Gene: pgk / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RBS3, phosphoglycerate kinase |
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#2: Chemical | ChemComp-3PG / |
#3: 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: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 30% polyethylene glycol (PEG) 4000, 0.2 M MgCl2 and 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46 Å / Num. obs: 61709 / % possible obs: 99.4 % / Redundancy: 3.3 % / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.18 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vpe Resolution: 2.1→16.887 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→16.887 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: 55.225 Å / Origin y: 6.5017 Å / Origin z: 0.8257 Å
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Refinement TLS group | Selection details: all |