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Yorodumi- PDB-4hnc: P. putida C92S/K166C/C264S mandelate racemase co-crystallized wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hnc | ||||||
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Title | P. putida C92S/K166C/C264S mandelate racemase co-crystallized with benzilic acid | ||||||
Components | Mandelate racemase | ||||||
Keywords | ISOMERASE / Enolase superfamily enzyme | ||||||
Function / homology | Function and homology information mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.889 Å | ||||||
Authors | Lietzan, A.D. / St.Maurice, M. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode. Authors: Nagar, M. / Lietzan, A.D. / St Maurice, M. / Bearne, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hnc.cif.gz | 159.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hnc.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hnc_validation.pdf.gz | 456.4 KB | Display | wwPDB validaton report |
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Full document | 4hnc_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 4hnc_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 4hnc_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/4hnc ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hnc | HTTPS FTP |
-Related structure data
Related structure data | 4fp1C 4m6uC 2mnrS 4fp0 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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-Components
#1: Protein | Mass: 41246.457 Da / Num. of mol.: 2 / Mutation: C92S, K166C, C264S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlA / Plasmid: pET-52b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11444, mandelate racemase #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: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% (w/v) PEG1500, 150 mM glycine, 50 mM NaCl, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2011 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.889→50 Å / Num. all: 75403 / Num. obs: 75062 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.889→1.92 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MNR Resolution: 1.889→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.257 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 17.849 Å2
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Refinement step | Cycle: LAST / Resolution: 1.889→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.889→1.938 Å / Total num. of bins used: 20
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