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Yorodumi- PDB-1xpy: Structural Basis for Catalytic Racemization and Substrate Specifi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xpy | ||||||
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Title | Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans | ||||||
Components | N-acylamino acid racemase | ||||||
Keywords | ISOMERASE / RACEMASE | ||||||
Function / homology | Function and homology information 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 | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, W.-C. / Chiu, W.-C. / Hsu, S.-K. / Wu, C.-L. / Chen, C.-Y. / Liu, J.-S. / Hsu, W.-H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans Authors: Wang, W.-C. / Chiu, W.-C. / Hsu, S.-K. / Wu, C.-L. / Chen, C.-Y. / Liu, J.-S. / Hsu, W.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xpy.cif.gz | 301.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xpy.ent.gz | 243.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/1xpy ftp://data.pdbj.org/pub/pdb/validation_reports/xp/1xpy | HTTPS FTP |
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-Related structure data
Related structure data | 1r0mSC 1xs2C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41060.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Plasmid: NAAAR-PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9RYA6 #2: Chemical | ChemComp-MG / #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: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: lithium sulfate, PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 1416552 / Num. obs: 66037 / % possible obs: 98.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R0M Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.712 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.229 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.881 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.362 Å / Total num. of bins used: 20 /
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