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- PDB-5fjr: N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fjr | ||||||
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Title | N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl napthylalanine | ||||||
![]() | O-SUCCINYLBENZOATE SYNTHASE | ||||||
![]() | LYASE / RACEMASE / N-ACYLAMINO ACID / ISOMERASE | ||||||
Function / homology | ![]() o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sanchez Carron, G. / Campopiano, D. / Grogan, G. | ||||||
![]() | ![]() Title: Structure of N-Acylamino Acid Racemase Mutants in Complex with Substrates Authors: Sanchez-Carron, G. / Campopiano, D. / Grogan, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.9 KB | Display | ![]() |
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PDB format | ![]() | 237.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5fjoC ![]() 5fjpC ![]() 5fjtC ![]() 5fjuC ![]() 4a6gS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 39447.219 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NPQ / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Sequence details | MUTATIONS Q26A,M50I,G291D,F323Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.7 % / Description: NONE |
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Crystal grow | pH: 8 Details: 100 MM TRIS HCL PH 8.0; 15% (W/V) PEG 4K; 800 MM SODIUM FORMATE; PROTEIN AT 8 MG PER ML |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→153.25 Å / Num. obs: 88697 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.44→2.5 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4A6G Resolution: 2.44→107.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.016 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.203 / 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: 49.197 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→107.89 Å
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Refine LS restraints |
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