+Open data
-Basic information
Entry | Database: PDB / ID: 1n2m | ||||||
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Title | The S53A Proenzyme Structure of Methanococcus jannaschii. | ||||||
Components | Pyruvoyl-dependent arginine decarboxylase | ||||||
Keywords | LYASE / pyruvoyl group / pyruvate / agmatine / arginine decarboxylase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n2m.cif.gz | 197.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n2m.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2m ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2m | HTTPS FTP |
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-Related structure data
Related structure data | 1mt1SC 1n13C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 proenzyme trimers are in the asymmetric unit. |
-Components
#1: Protein | Mass: 17708.564 Da / Num. of mol.: 6 / Mutation: S53A Source method: isolated from a genetically manipulated source Details: proenzyme form Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0316 / Plasmid: pET19b (Novagen) / Production host: Escherichia coli (E. coli) Strain (production host): BL21-Codon-Plus(DE3)-RIL (Stratagene) References: UniProt: Q57764, arginine decarboxylase #2: Chemical | ChemComp-MRD / ( #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: 2.01 Å3/Da / Density % sol: 38.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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-ethansulfonic 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-ethansulfonic 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: CHESS / Beamline: A1 / Wavelength: 0.947 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2002 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.947 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28.7 Å / Num. all: 68424 / Num. obs: 61718 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.061 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.85 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 3497 / Rsym value: 0.262 / % possible all: 51.5 |
Reflection | *PLUS Num. measured all: 187377 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 51.5 % / Rmerge(I) obs: 0.262 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MT1 Resolution: 1.9→28.69 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.2446 Å2 / ksol: 0.413056 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.97 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.233 |