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Yorodumi- PDB-5fjt: N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fjt | ||||||
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Title | N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D F323 mutant in complex with N-acetyl phenylalanine | ||||||
Components | O-SUCCINYLBENZOATE SYNTHASE | ||||||
Keywords | LYASE / ISOMERASE / RACEMASE / N-ACYL AMINO ACID | ||||||
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: 2.11 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 | 5fjt.cif.gz | 290 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjt.ent.gz | 235.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fjt_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 5fjt_full_validation.pdf.gz | 487.4 KB | Display | |
Data in XML | 5fjt_validation.xml.gz | 57.1 KB | Display | |
Data in CIF | 5fjt_validation.cif.gz | 80.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjt ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjt | HTTPS FTP |
-Related structure data
Related structure data | 5fjoC 5fjpC 5fjrC 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39522.305 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS SP. (bacteria) / Strain: TS-1-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44244, o-succinylbenzoate synthase #2: Chemical | ChemComp-5CR / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Sequence details | MUTATIONS G291D F323Y | |
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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: 3.7 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→88 Å / Num. obs: 133075 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.11→2.14 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 6.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A6G Resolution: 2.11→151.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.932 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.118 / 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: 34.898 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→151.68 Å
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Refine LS restraints |
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