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- PDB-3kkk: Y92C catalytic residue mutant of Phosphoglycerate Mutase from Pla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kkk | ||||||
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Title | Y92C catalytic residue mutant of Phosphoglycerate Mutase from Plasmodium falciparum | ||||||
![]() | Phosphoglycerate mutase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
![]() | ![]() Title: Structure of a phosphoglycerate mutase from Plasmodium falciparum Authors: Larson, E.T. / Caruthers, J.M. / Zhang, L. / Hol, W.G.J. / Merritt, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.2 KB | Display | ![]() |
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PDB format | ![]() | 157.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1xq9S 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 29787.223 Da / Num. of mol.: 4 / Mutation: Y92C Source method: isolated from a genetically manipulated source Details: N-terminal 6xHis tag added during cloning, Y92C mutation confirmed from plasmid sequence Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 35% PEG 1000, 0.1 M HEPES pH 7.2, 0.1 M KSCN, 5 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 20, 2007 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.08→50 Å / Num. obs: 64085 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.045 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.22 / Num. unique all: 6390 / Χ2: 1.005 / % possible all: 99.8 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1xq9 Resolution: 2.08→31.46 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.107 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.19 Å2 / Biso mean: 26.78 Å2 / Biso min: 2.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→31.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.131 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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