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Yorodumi- PDB-1s9r: CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s9r | ||||||
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Title | CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH A REACTION INTERMEDIATE | ||||||
Components | Arginine deiminase | ||||||
Keywords | HYDROLASE / DEIMINASE / 5-FOLD PSEUDO-SYMMETRIC DOMAIN / 5-HELIX BUNDLE DOMAIN / RACTION INTERMEDIATE | ||||||
Function / homology | Function and homology information arginine deiminase / arginine deiminase activity / arginine deiminase pathway / arginine catabolic process to ornithine / cytoplasm Similarity search - Function | ||||||
Biological species | Mycoplasma arginini (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å | ||||||
Authors | Das, K. / Buttler, G.H. / Kwiatkowski, V. / Clark Jr., A.D. / Yadav, P. / Arnold, E. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structures of Arginine Deiminase with Covalent Reaction Intermediates: Implications for Catalytic Mechanism Authors: Das, K. / Buttler, G.H. / Kwiatkowski, V. / Clark Jr., A.D. / Yadav, P. / Arnold, E. | ||||||
History |
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Remark 600 | HETEROGEN THE MOLECULE IS A REACTION INTERMEDIATE FROM THE ENZYMATIC CONVERSION OF L-ARGININE TO L- ...HETEROGEN THE MOLECULE IS A REACTION INTERMEDIATE FROM THE ENZYMATIC CONVERSION OF L-ARGININE TO L-CITRULLINE. THIS MOLECULE LOST AN NH2 GROUP AND IS COVALENTLY ATTACHED TO CYS407. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s9r.cif.gz | 190.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s9r.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s9r_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 1s9r_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 1s9r_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 1s9r_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/1s9r ftp://data.pdbj.org/pub/pdb/validation_reports/s9/1s9r | HTTPS FTP |
-Related 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: 46563.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: 5-FOLD PSEUDOSYMMETRIC GUANIDINO GROUP MODIFYING ENZYME Source: (natural) Mycoplasma arginini (bacteria) / References: UniProt: P23793, arginine deiminase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UNX / #5: 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: 4.68 Å3/Da / Density % sol: 73.52 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6000, POTASSIUM PHOSPHATE, ARGININE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 116186 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2.82 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.354 / Num. unique all: 5649 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→19.46 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 293988.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.7725 Å2 / ksol: 0.383494 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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