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- PDB-2xgz: Engineering the enolase active site pocket: Crystal structure of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xgz | ||||||
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Title | Engineering the enolase active site pocket: Crystal structure of the S39N D321R mutant of yeast enolase 1 | ||||||
![]() | ENOLASE 1![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() regulation of vacuole fusion, non-autophagic / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schreier, B. / Hocker, B. | ||||||
![]() | ![]() Title: Engineering the Enolase Magnesium II Binding Site -Implications for its Evolution. Authors: Schreier, B. / Hoecker, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.1 KB | Display | ![]() |
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PDB format | ![]() | 151.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xh0C ![]() 2xh2C ![]() 2xh4C ![]() 2xh7C ![]() 2oneS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 47757.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-437 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: PET-21 / Production host: ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 40 TO ASN ENGINEERED RESIDUE IN CHAIN A, ASP 322 TO ARG ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 Details: 20% PEG 8000, 0.2M SODIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→40 Å / Num. obs: 64875 / % possible obs: 75.9 % / Observed criterion σ(I): 2 / Redundancy: 1.65 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.66 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.05 / % possible all: 76.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2ONE Resolution: 1.8→37.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.795 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / 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: 16.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.9 Å
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Refine LS restraints |
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