+Open data
-Basic information
Entry | Database: PDB / ID: 4dg5 | ||||||
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Title | Crystal structure of staphylococcal Phosphoglycerate kinase | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | TRANSFERASE / Bi-lobal protein / ATP Synthesis / phosphorylation / cytosol | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Roychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K. | ||||||
Citation | Journal: To be Published Title: Structure based functional analysis of Staphylococcal Phosphoglycerate kinase Authors: Roychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dg5.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dg5.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 4dg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dg5_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 4dg5_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 4dg5_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 4dg5_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/4dg5 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/4dg5 | HTTPS FTP |
-Related structure data
Related structure data | 1phpS 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: 43499.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: pgk, SAR0829 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q6GIL7, 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: 2.26 Å3/Da / Density % sol: 45.66 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.15M Calcium chloride dihydrate, 0.1M HEPES-Na, 20% (w/v)Polyethylene glycol 2000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2010 / Details: Varimax mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→58.373 Å / Num. all: 16871 / Num. obs: 16871 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.094 / Net I/σ(I): 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHP Resolution: 2.3→58.37 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.842 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.015 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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 max: 500 Å2 / Biso mean: 15.703 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→58.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -3.9813 Å / Origin y: 8.927 Å / Origin z: -23.8766 Å
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