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- PDB-2x5f: Crystal structure of the methicillin-resistant Staphylococcus aur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x5f | ||||||
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Title | Crystal structure of the methicillin-resistant Staphylococcus aureus Sar2028, an aspartate_tyrosine_phenylalanine pyridoxal-5'-phosphate dependent aminotransferase | ||||||
![]() | ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
![]() | ![]() Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an ...Title: Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an Aspartate/Tyrosine/Phenylalanine Pyridoxal-5'-Phosphate-Dependent Aminotransferase. Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G. ...Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G.L. / White, M.F. / Barton, G.J. / Coote, P.J. / Naismith, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 346.8 KB | Display | ![]() |
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PDB format | ![]() | 286 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.7 KB | Display | ![]() |
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Full document | ![]() | 482.3 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ivyC ![]() 2jg5C ![]() 2jg6C ![]() 2vw8C ![]() 2vxzC ![]() 2wj9C ![]() 2x0oC ![]() 2x3dC ![]() 2x3eC ![]() 2x3fC ![]() 2x3gC ![]() 2x3lC ![]() 2x3mC ![]() 2x3nC ![]() 2x3oC ![]() 2x48C ![]() 2x4gC ![]() 2x4hC ![]() 2x4iC ![]() 2x4jC ![]() 2x4kC ![]() 2x4lC ![]() 2x5cC ![]() 2x5dC ![]() 2x5gC ![]() 2x5hC ![]() 2x5pC ![]() 2x5qC ![]() 2x5rC ![]() 2x5tC ![]() 2x7bC ![]() 2x7iC ![]() 2xu2C C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 2 / Auth seq-ID: 4 - 33 / Label seq-ID: 6 - 35
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48346.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 236 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): THERE IS AN OXYGEN ATOM MISSING FROM PLP |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.18 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 28% PEG3350, 0.1M HEPES PH 7.5. THE CRYSTALS WERE CRYOPROTECTED WITH 16% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.24 Å / Num. obs: 69033 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.01 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.8→27.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.395 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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 mean: 7.184 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.24 Å
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Refine LS restraints |
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