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- PDB-4bq0: Pseudomonas aeruginosa beta-alanine:pyruvate aminotransferase hol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bq0 | ||||||
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Title | Pseudomonas aeruginosa beta-alanine:pyruvate aminotransferase holoenzyme without divalent cations on dimer-dimer interface | ||||||
![]() | BETA-ALANINE--PYRUVATE TRANSAMINASE | ||||||
![]() | TRANSFERASE / PSEUDO-TRANSLATION | ||||||
Function / homology | ![]() beta-alanine-pyruvate transaminase / beta-alanine-pyruvate transaminase activity / beta-alanine biosynthetic process / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Isupov, M.N. / Lebedev, A.A. / Westlake, A. / Sayer, C. / Littlechild, J.A. | ||||||
![]() | ![]() Title: Space-Group and Origin Ambiguity in Macromolecular Structures with Pseudo-Symmetry and its Treatment with the Program Zanuda. Authors: Lebedev, A.A. / Isupov, M.N. #1: ![]() Title: Structural Studies of Pseudomonas and Chromobacterium Omega-Aminotransferases Provide Insights Into Their Differing Substrate Specificity. Authors: Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.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 | ![]() | 389.2 KB | Display | ![]() |
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PDB format | ![]() | 320.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.3 KB | Display | ![]() |
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Full document | ![]() | 506.3 KB | Display | |
Data in XML | ![]() | 83.9 KB | Display | |
Data in CIF | ![]() | 124.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b9bS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 48432.887 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): COFACTOR PLP WAS NOT MODELLED TO FORM A SCHIFF BASE LINK ,INTERNAL ...PYRIDOXAL-5'-PHOSPHATE (PLP): COFACTOR PLP WAS NOT MODELLED TO FORM A SCHIFF BASE LINK ,INTERNAL ALDIMINE, TO THE CATALYTIC LYS288. THE OCCUPANCY REFINEMENT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.9 % / Description: NONE |
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Crystal grow | Method: microbatch / pH: 5.5 Details: 10 MG/ML PROTEIN, 50MM SODIUM CHLORIDE, 30 MM PYRUVATE, 100 MM SODIUM CITRATE, 20% W/V PEG 3000, PH 5.5, MICROBATCH CRYSTALLIZATION METHOD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→64 Å / Num. obs: 2104915 / % possible obs: 99 % / Redundancy: 13.2 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.1 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4B9B Resolution: 1.77→63.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.504 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.162 / 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: 25.264 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→63.37 Å
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Refine LS restraints |
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