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Yorodumi- PDB-4pxo: Crystal structure of Maleylacetoacetate isomerase from Methylobac... -
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-Basic information
Entry | Database: PDB / ID: 4pxo | ||||||
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Title | Crystal structure of Maleylacetoacetate isomerase from Methylobacteriu extorquens AM1 WITH BOUND MALONATE AND GSH (TARGET EFI-507068) | ||||||
Components | Maleylacetoacetate isomerase (Glutathione S-transferase) | ||||||
Keywords | TRANSFERASE / GLUTATHIONE S-TRANSFERASE ZETA / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information maleylacetoacetate isomerase / maleylacetoacetate isomerase activity / aromatic amino acid metabolic process / glutathione transferase / glutathione transferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of glutathione s-transferase zeta from Methylobacterium extorquens (TARGET EFI-507068) Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / 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 | 4pxo.cif.gz | 194 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pxo.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pxo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4pxo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4pxo_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 4pxo_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/4pxo ftp://data.pdbj.org/pub/pdb/validation_reports/px/4pxo | HTTPS FTP |
-Related structure data
Related structure data | 4px1S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 26287.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: ATCC 14718 / DSM 1338 / AM1 / Gene: maiA, MexAM1_META1p2830 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C5ATQ9, glutathione transferase, maleylacetoacetate isomerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #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: 3.08 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | pH: 8.5 Details: PROTEIN (10 MM TRIS, 150 MM NACL, 5% GLYCEROL, 5 MM DTT); RESERVOIR (0.1 M HEPES-NAOH, PH 7.0, 1.1M SODIUM MALONATE, 0.5% (v/v) Jeffamine ED-2001 (MCSG2 B10), 10 MM GSH; CRYOPROTECTION: ...Details: PROTEIN (10 MM TRIS, 150 MM NACL, 5% GLYCEROL, 5 MM DTT); RESERVOIR (0.1 M HEPES-NAOH, PH 7.0, 1.1M SODIUM MALONATE, 0.5% (v/v) Jeffamine ED-2001 (MCSG2 B10), 10 MM GSH; CRYOPROTECTION: (RESERVOIR), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-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: Mar 14, 2014 / 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: 1.8→50 Å / Num. obs: 61218 / % possible obs: 99.7 % / Observed criterion σ(I): -5 / Redundancy: 14.4 % / Biso Wilson estimate: 21.628 Å2 / Rsym value: 0.101 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4PX1 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.739 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.344 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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