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Yorodumi- PDB-4kdy: Crystal structure of maleylacetoacetate isomerase from Anaeromyxo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kdy | ||||||
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Title | Crystal structure of maleylacetoacetate isomerase from Anaeromyxobacter dehalogenans 2CP-1, Target EFI-507175, with bound GSH in the active site | ||||||
Components | Maleylacetoacetate isomerase | ||||||
Keywords | ISOMERASE / Structural Genomics / Enzyme Function Initiative / EFI / GSH | ||||||
Function / homology | Function and homology information maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase activity / glutathione metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Anaeromyxobacter dehalogenans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of maleylacetoacetate isomerase from Anaeromyxobacter dehalogenans 2CP-1, Target EFI-507175, with bound GSH in the active site Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kdy.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kdy.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 4kdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/4kdy ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kdy | HTTPS FTP |
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-Related structure data
Related structure data | 4igjS 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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-Components
#1: Protein | Mass: 27588.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaeromyxobacter dehalogenans (bacteria) Strain: 2CP-1 / ATCC BAA-258 / Gene: A2cp1_3570 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8J605, maleylacetoacetate isomerase #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Chemical | #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: 2.03 Å3/Da / Density % sol: 39.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M ammonium citrate dibasic, pH 5.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 6, 2013 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 72817 / Num. obs: 72580 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4IGJ Resolution: 1.5→31.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.146 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 21.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→31.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.536 Å / Total num. of bins used: 20
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