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Yorodumi- PDB-4nwx: Crystal structure of phosphoglycerate mutase from Staphylococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nwx | ||||||
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Title | Crystal structure of phosphoglycerate mutase from Staphylococcus aureus in 2-phosphoglyceric acid bound form | ||||||
Components | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase | ||||||
Keywords | ISOMERASE / Glycolytic enzyme / Cytosol | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Roychowdhury, A. / Kundu, A. / Bose, M. / Gujar, A. / Das, A.K. | ||||||
Citation | Journal: Febs J. / Year: 2015 Title: Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism Authors: Roychowdhury, A. / Kundu, A. / Bose, M. / Gujar, A. / Mukherjee, S. / 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 | 4nwx.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nwx.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nwx_validation.pdf.gz | 463.2 KB | Display | wwPDB validaton report |
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Full document | 4nwx_full_validation.pdf.gz | 470.9 KB | Display | |
Data in XML | 4nwx_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4nwx_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/4nwx ftp://data.pdbj.org/pub/pdb/validation_reports/nw/4nwx | HTTPS FTP |
-Related structure data
Related structure data | 4my4SC 4nwjC 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: 57460.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: NCTC8325 / Gene: gpmI, SAOUHSC_00798 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q2G029, phosphoglycerate mutase (2,3-diphosphoglycerate-independent) | ||||
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#2: Chemical | ChemComp-2PG / | ||||
#3: Chemical | #4: Chemical | ChemComp-DTT / | #5: 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: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.2M NaCl, Bis-tris, 25%(w/v) PEG3350, pH 6.3, 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: Nov 14, 2013 / Details: Varimax (osmic mirror) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: varimax with osmic mirror optics. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.01→60.804 Å / Num. all: 37033 / Num. obs: 37033 / % possible obs: 99.1 % / Redundancy: 7.1 % / Rsym value: 0.1 / Net I/σ(I): 19.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 4MY4 Resolution: 2.01→19.64 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.526 / SU ML: 0.098 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.521 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→19.64 Å
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Refine LS restraints |
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