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Yorodumi- PDB-2wm1: The crystal structure of human alpha-amino-beta-carboxymuconate- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wm1 | ||||||
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Title | The crystal structure of human alpha-amino-beta-carboxymuconate- epsilon-semialdehyde decarboxylase in complex with 1,3- dihydroxyacetonephosphate suggests a regulatory link between NAD synthesis and glycolysis | ||||||
Components | 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE | ||||||
Keywords | LYASE / NEUROLOGICAL DISORDERS / METAL-DEPENDENT AMIDOHYDROLASE / KYNURENINE PATHWAY / ALTERNATIVE SPLICING / QUINOLINIC ACID / NAD BIOSYNTHESIS / CEREBRAL MALARIA / DECARBOXYLASE / PICOLINIC ACID / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information aminocarboxymuconate-semialdehyde decarboxylase / aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from tryptophan / secondary metabolic process / tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding ...aminocarboxymuconate-semialdehyde decarboxylase / aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from tryptophan / secondary metabolic process / tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Garavaglia, S. / Perozzi, S. / Galeazzi, L. / Raffaelli, N. / Rizzi, M. | ||||||
Citation | Journal: FEBS J. / Year: 2009 Title: The Crystal Structure of Human Alpha-Amino-Beta-Carboxymuconate-Epsilon-Semialdehyde Decarboxylase in Complex with 1,3-Dihydroxyacetonephosphate Suggests a Regulatory Link between Nad Synthesis and Glycolysis Authors: Garavaglia, S. / Perozzi, S. / Galeazzi, L. / Raffaelli, N. / Rizzi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wm1.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wm1.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wm1_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 2wm1_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 2wm1_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2wm1_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/2wm1 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/2wm1 | HTTPS FTP |
-Related structure data
Related structure data | 2hbvS 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
#1: Protein | Mass: 38084.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): GS115 / Production host: PICHIA PASTORIS (fungus) References: UniProt: Q8TDX5, aminocarboxymuconate-semialdehyde decarboxylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-13P / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | LAST FOUR C-TERMINAL RESIDUES NOT VISIBLE IN THE ELECTRON DENSITY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 24525 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.8 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HBV Resolution: 2.01→43.11 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.867 / SU B: 4.161 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.188 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→43.11 Å
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