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Yorodumi- PDB-3r0k: Crystal structure of NYSGRC enolase target 200555, a putative dip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r0k | |||||||||
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Title | Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Tartrate bound, no Mg | |||||||||
Components | Enzyme of enolase superfamily | |||||||||
Keywords | METAL BINDING PROTEIN / structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | |||||||||
Function / homology | Function and homology information racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Francisella philomiragia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Vetting, M.W. / Hillerich, B. / Seidel, R.D. / Zencheck, W.D. / Toro, R. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r0k.cif.gz | 291.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r0k.ent.gz | 248.8 KB | Display | PDB format |
PDBx/mmJSON format | 3r0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r0k_validation.pdf.gz | 477 KB | Display | wwPDB validaton report |
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Full document | 3r0k_full_validation.pdf.gz | 483.8 KB | Display | |
Data in XML | 3r0k_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 3r0k_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/3r0k ftp://data.pdbj.org/pub/pdb/validation_reports/r0/3r0k | HTTPS FTP |
-Related structure data
Related structure data | 3ijiC 3ijlC 3ijqC 3ik4C 3jvaC 3jw7C 3jzuC 3k1gC 3kumC 3q45C 3q4dC 3r0uC 3r10C 3r11C 3r1zC 3ritC 3ro6C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42455.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella philomiragia (bacteria) / Strain: subsp. philomiragia / Gene: Fphi_1647 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R-RIL / References: UniProt: B0TZW0 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-TAR / | #4: Chemical | ChemComp-GOL / #5: 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: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Protein (10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir (2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate), Soak (2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5. ...Details: Protein (10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir (2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate), Soak (2.4 M Ammonium sulfate, 100 mM NaCitrate pH 5.6, KNaTartrate, 20% glycerol, 10 min, vapor diffusion, sitting drop, temperature 294K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97905 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Details: Undulator Source |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 75038 / Num. obs: 75038 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.8 % / Biso Wilson estimate: 21.61 Å2 / Rsym value: 0.093 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 27.9 % / Mean I/σ(I) obs: 11.9 / Num. unique all: 10818 / Rsym value: 0.312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→28.103 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8895 / SU ML: 0.18 / σ(F): 0 / Phase error: 17.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.201 Å2 / ksol: 0.392 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.56 Å2 / Biso mean: 28.2443 Å2 / Biso min: 6.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.103 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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