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Yorodumi- PDB-4b9b: The structure of the omega aminotransferase from Pseudomonas aeru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b9b | ||||||
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Title | The structure of the omega aminotransferase from Pseudomonas aeruginosa | ||||||
Components | BETA-ALANINE-PYRUVATE TRANSAMINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural Studies with 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b9b.cif.gz | 793.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b9b.ent.gz | 660.6 KB | Display | PDB format |
PDBx/mmJSON format | 4b9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b9b_validation.pdf.gz | 515.2 KB | Display | wwPDB validaton report |
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Full document | 4b9b_full_validation.pdf.gz | 572.5 KB | Display | |
Data in XML | 4b9b_validation.xml.gz | 178.7 KB | Display | |
Data in CIF | 4b9b_validation.cif.gz | 269 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b9b ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b9b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 48432.887 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: A3LGU8, UniProt: Q9I700*PLUS, beta-alanine-pyruvate transaminase |
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-Non-polymers , 5 types, 4604 molecules
#2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.47 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→42 Å / Num. obs: 393083 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.64→66.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.308 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / 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: 16.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→66.58 Å
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Refine LS restraints |
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