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Yorodumi- PDB-1d7k: CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d7k | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION | ||||||
Components | HUMAN ORNITHINE DECARBOXYLASE | ||||||
Keywords | LYASE / ALPHA-BETA BARREL / PYRIDOXAL 5'-PHOSPHATE / SHEET-DOMAIN / DECARBOXYLATION / ORNITHINE | ||||||
Function / homology | Function and homology information ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation ...ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation / positive regulation of cell population proliferation / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Almrud, J.J. / Oliveira, M.A. / Kern, A.D. / Grishin, N.V. / Phillips, M.A. / Hackert, M.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding. Authors: Almrud, J.J. / Oliveira, M.A. / Kern, A.D. / Grishin, N.V. / Phillips, M.A. / Hackert, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d7k.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d7k.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 1d7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d7k_validation.pdf.gz | 386.5 KB | Display | wwPDB validaton report |
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Full document | 1d7k_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 1d7k_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1d7k_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d7k ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d7k | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47161.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P11926, ornithine decarboxylase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.5 Details: 20% PEG 3350, 0.2M NaCl, 5mM DTT, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 16K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 55799 / Num. obs: 53656 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.363 / Num. unique all: 4929 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 223151 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Resolution: 2.1→30.5 Å / Cross valid method: throyghout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: This structure was refined using data from 30-2.1 angstrom resolution using the CCP4 suite program REFMAC. The REFMAC refinement was carried out using the maximum likelihood function and ...Details: This structure was refined using data from 30-2.1 angstrom resolution using the CCP4 suite program REFMAC. The REFMAC refinement was carried out using the maximum likelihood function and minimization by the conjugate direction method.
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Refinement step | Cycle: LAST / Resolution: 2.1→30.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.235 / Num. reflection obs: 6009 |