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Yorodumi- PDB-4ofc: 2.0 Angstroms X-ray crystal structure of human 2-amino-3-carboxym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ofc | ||||||
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Title | 2.0 Angstroms X-ray crystal structure of human 2-amino-3-carboxymuconate-6-semialdehye decarboxylase | ||||||
Components | 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase | ||||||
Keywords | OXIDOREDUCTASE / TIM-barrel / Decarboxylase | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Huo, L. / Liu, F. / Iwaki, H. / Chen, L. / Hasegawa, Y. / Liu, A. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: Human alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD): A structural and mechanistic unveiling. Authors: Huo, L. / Liu, F. / Iwaki, H. / Li, T. / Hasegawa, Y. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ofc.cif.gz | 415.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ofc.ent.gz | 339.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ofc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/4ofc ftp://data.pdbj.org/pub/pdb/validation_reports/of/4ofc | HTTPS FTP |
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-Related structure data
Related structure data | 4ignC 4ih3SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 37955.109 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACMSD / Production host: Escherichia coli (E. coli) References: UniProt: Q8TDX5, aminocarboxymuconate-semialdehyde decarboxylase #2: Chemical | ChemComp-ZN / #3: 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: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Bis-Tris, 22% PEG 3350, 0.2 M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→45 Å / Num. all: 150018 / Num. obs: 131416 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.153 |
Reflection shell | Resolution: 1.99→2.03 Å / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4IH3 Resolution: 1.99→27.106 Å / FOM work R set: 0.8235 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.925 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.97 Å2 / Biso mean: 29.88 Å2 / Biso min: 11.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→27.106 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: 30
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