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Yorodumi- PDB-1mt1: The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mt1 | |||||||||
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Title | The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii | |||||||||
Components |
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Keywords | LYASE / pyruvoyl group / pyruvate / agmatine / arginine | |||||||||
Function / homology | Function and homology information arginine decarboxylase / arginine decarboxylase activity / arginine catabolic process Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | |||||||||
Authors | Tolbert, W.D. / Graham, D.E. / White, R.H. / Ealick, S.E. | |||||||||
Citation | Journal: Structure / Year: 2003 Title: Pyruvoyl-Dependent Arginine Decarboxylase from Methanococcus jannaschii: Crystal Structures of the Self-Cleaved and S53A Proenzyme Forms Authors: Tolbert, W.D. / Graham, D.E. / White, R.H. / Ealick, S.E. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis. Authors: Graham, D.E. / Xu, H. / White, R.H. | |||||||||
History |
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Remark 999 | SEQUENCE Each monomer undergoes an internal self cleavage reaction which generates a pyruvoyl ...SEQUENCE Each monomer undergoes an internal self cleavage reaction which generates a pyruvoyl cofactor. RESIDUE 53 IS CONVERTED TO A PYRUVOYL GROUP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mt1.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mt1.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mt1_validation.pdf.gz | 506.4 KB | Display | wwPDB validaton report |
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Full document | 1mt1_full_validation.pdf.gz | 518.1 KB | Display | |
Data in XML | 1mt1_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 1mt1_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mt1 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mt1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Two (alpha beta)3 trimers are located in the asymmetric unit. Each monomer undergoes an internal self cleavage reaction which generates a pyruvoyl cofactor. |
-Components
#1: Protein | Mass: 5475.011 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0316 / Plasmid: pET19b (Novagen) / Production host: Escherichia coli (E. coli) Strain (production host): BL21-CodonPlus(DE3)-RIL (Stratagene) References: UniProt: Q57764, arginine decarboxylase #2: Protein | Mass: 12531.892 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0316 / Plasmid: pET19b (Novagen) / Production host: Escherichia coli (E. coli) Strain (production host): BL21-CodonPlus(DE3)-RIL (Stratagene) References: UniProt: Q57764, arginine decarboxylase #3: Chemical | ChemComp-AG2 / #4: 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: 2.12 Å3/Da / Density % sol: 42.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta octyl glucoside, putrescine, ethylenediaminetetraacetic acid dithiothreitol, pH 7. ...Details: PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta octyl glucoside, putrescine, ethylenediaminetetraacetic acid dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 8-BM / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→63.5 Å / Num. all: 57557 / Num. obs: 57557 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.142 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.11→2.24 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 8398 / Rsym value: 0.383 / % possible all: 100 |
Reflection | *PLUS Num. obs: 52185 / % possible obs: 100 % / Num. measured all: 368924 / Rmerge(I) obs: 0.142 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.383 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: none Resolution: 2.2→63.5 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Data was refined to the MLHL target in CNS. The number of reflections reported includes anomalous data.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.4748 Å2 / ksol: 0.361126 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→63.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.28 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.204 |