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Yorodumi- PDB-5fjo: N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fjo | ||||||
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Title | N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl naphthylalanine | ||||||
Components | N-succinylamino acid racemase | ||||||
Keywords | LYASE / RACEMASE / ACYL AMINO ACID / ISOMERASE / AMYCOLATOPSIS | ||||||
Function / homology | Function and homology information O-succinylbenzoate synthase activity / o-succinylbenzoate synthase / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Amycolatopsis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Sanchez-Carron, G. / Campopiano, D. / Grogan, G. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjo.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjo.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fjo_validation.pdf.gz | 1002.8 KB | Display | wwPDB validaton report |
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Full document | 5fjo_full_validation.pdf.gz | 1013.1 KB | Display | |
Data in XML | 5fjo_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 5fjo_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjo ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjo | HTTPS FTP |
-Related structure data
Related structure data | 5fjpC 5fjrC 5fjtC 5fjuC 4a6gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8742, -0.4856, 0.005101), Vector: |
-Components
#1: Protein | Mass: 39522.305 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis sp. (bacteria) / Strain: TS-1-60 / Gene: Aaar / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q44244, Isomerases; Racemases and epimerases; Acting on amino acids and derivatives, o-succinylbenzoate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.7 % / Description: NONE |
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Crystal grow | pH: 8 Details: 100 MM TRIS HCL PH 8.0, 15% 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Date: Dec 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→68.55 Å / Num. obs: 69708 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A6G Resolution: 2.08→68.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.8 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / 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: 21.579 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→68.55 Å
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Refine LS restraints |
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