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Yorodumi- PDB-4ihc: Crystal structure of probable mannonate dehydratase Dd703_0947 (t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ihc | ||||||
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Title | Crystal structure of probable mannonate dehydratase Dd703_0947 (target EFI-502222) from Dickeya dadantii Ech703 | ||||||
Components | Mandelate racemase/muconate lactonizing protein | ||||||
Keywords | ISOMERASE / dehydratase / magnesium binding / Structural Genomics / Enzyme Function Initiative / EFI | ||||||
Function / homology | Function and homology information gluconate dehydratase / gluconate dehydratase activity / mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Dickeya dadantii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N.F. / Stead, M. / Love, J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of mannonate dehydratase Dd703_0947 from Dickeya dadantii Ech703 Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N.F. / Stead, M. / Love, J. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ihc.cif.gz | 659.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ihc.ent.gz | 538.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ihc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/4ihc ftp://data.pdbj.org/pub/pdb/validation_reports/ih/4ihc | HTTPS FTP |
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-Related structure data
Related structure data | 3tw9S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 48891.637 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: Ech703 / Gene: Dd703_0947 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6CBG9 |
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-Non-polymers , 6 types, 2037 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-IOD / #6: Chemical | ChemComp-CL / #7: 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: 2.79 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M AMMONIUM IODIDE, PH 7.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2012 / Details: MIRRORS |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 277432 / % possible obs: 88.2 % / Observed criterion σ(I): -5 / Redundancy: 2.6 % / Rsym value: 0.19 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1 / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TW9 Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.942 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.159 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.887 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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