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Yorodumi- PDB-2z0i: Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z0i | ||||||
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Title | Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus | ||||||
Components | Delta-aminolevulinic acid dehydratase | ||||||
Keywords | LYASE / DEHYDRATASE / TETRAPYRROLE BIOSYNTHESIS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Heme biosynthesis / proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / negative regulation of proteasomal protein catabolic process / cellular response to lead ion / response to mercury ion / response to aluminum ion ...Heme biosynthesis / proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / negative regulation of proteasomal protein catabolic process / cellular response to lead ion / response to mercury ion / response to aluminum ion / response to selenium ion / protoporphyrinogen IX biosynthetic process / response to fatty acid / response to cobalt ion / response to methylmercury / response to arsenic-containing substance / response to metal ion / response to iron ion / response to herbicide / heme biosynthetic process / response to ionizing radiation / response to zinc ion / response to vitamin E / response to amino acid / response to cadmium ion / response to glucocorticoid / Neutrophil degranulation / cellular response to interleukin-4 / response to nutrient / response to organic substance / response to activity / protein homooligomerization / response to ethanol / response to oxidative stress / response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / extracellular space / zinc ion binding / metal ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Wang, H. / Xie, Y. / Kawazoe, M. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus Authors: Wang, H. / Xie, Y. / Kawazoe, M. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z0i.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z0i.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 2z0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z0i ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z0i | HTTPS FTP |
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-Related structure data
Related structure data | 1e51S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36549.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PX041202-30 / Production host: Cell-free protein synthesis References: UniProt: Q9DD05, UniProt: P10518*PLUS, porphobilinogen synthase #2: 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: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: TRIS, PEG 400, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 12792 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rsym value: 0.176 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1254 / Rsym value: 0.64 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+51 / Resolution: 3.2→42.68 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 25267.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1807 Å2 / ksol: 0.371122 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 47.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→42.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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