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- PDB-4rpf: Crystal structure of homoserine kinase from Yersinia pestis Nepal... -
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Basic information
Entry | Database: PDB / ID: 4rpf | ||||||
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Title | Crystal structure of homoserine kinase from Yersinia pestis Nepal516, NYSGRC target 032715 | ||||||
![]() | Homoserine kinase | ||||||
![]() | TRANSFERASE / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / KINASE | ||||||
Function / homology | ![]() homoserine kinase / homoserine kinase activity / threonine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ptskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Ptskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: Crystal Structure of Homoserine Kinase from Yersinia Pestis Nepal516, Nysgrc Target 032715 Authors: Patskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / ...Authors: Patskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 180.5 KB | Display | ![]() |
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PDB format | ![]() | 151.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 466.5 KB | Display | ![]() |
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Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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5 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 33347.250 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PROTEIN IN 10 MM BIS-TRIS, 500 MM SODIUM CHLORIDE, 10% GLYCEROL, 5 MM DTT, 10 MM D-GLUCOSE, RESERVOIR: 0.17 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE, PH 5.6, 25.5% W/V PEG4000, 15% W/V ...Details: PROTEIN IN 10 MM BIS-TRIS, 500 MM SODIUM CHLORIDE, 10% GLYCEROL, 5 MM DTT, 10 MM D-GLUCOSE, RESERVOIR: 0.17 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE, PH 5.6, 25.5% W/V PEG4000, 15% W/V GLYCEROL, 0.5 M 2-Aminoethylphosphonate; CRYOPROTECTANT = RESERVOIR, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014 / Details: MIRRORS | ||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 70518 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 18.25 | ||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.5 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.3→40.72 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.054 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.047 / 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: 1.1 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.805 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40.72 Å
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Refine LS restraints |
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