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Yorodumi- PDB-1j0b: Crystal Structure Analysis of the ACC deaminase homologue complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j0b | ||||||
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Title | Crystal Structure Analysis of the ACC deaminase homologue complexed with inhibitor | ||||||
Components | 1-aminocyclopropane-1-carboxylate deaminase | ||||||
Keywords | LYASE / PLP dependent | ||||||
Function / homology | Function and homology information 1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Fujino, A. / Ose, T. / Honma, M. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii Authors: Fujino, A. / Ose, T. / Yao, M. / Tokiwano, T. / Honma, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j0b.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1j0b.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 1j0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j0b_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1j0b_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 1j0b_validation.xml.gz | 263.6 KB | Display | |
Data in CIF | 1j0b_validation.cif.gz | 350.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j0b ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j0b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35232.824 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O57809, EC: 4.1.99.4 #2: Chemical | ChemComp-5PA / #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: 2.43 Å3/Da / Density % sol: 49.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, 2-propanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2001 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 245565 / Num. obs: 244791 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 58.82 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.047 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.2 / Num. unique all: 35772 / Rsym value: 0.276 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 39.1 Å / % possible obs: 100 % / Num. measured all: 244791 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 100 % / Num. unique obs: 35772 / Num. measured obs: 87298 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 52.687 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.79 Å
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.2918 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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