+Open data
-Basic information
Entry | Database: PDB / ID: 1g63 | ||||||
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Title | PEPTIDYL-CYSTEINE DECARBOXYLASE EPID | ||||||
Components | EPIDERMIN MODIFYING ENZYME EPID | ||||||
Keywords | OXIDOREDUCTASE / alpha / beta protein / Rossmann like fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Blaesse, M. / Kupke, T. / Huber, R. / Steinbac, S. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate. Authors: Blaesse, M. / Kupke, T. / Huber, R. / Steinbacher, S. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Molecular characterization of lantibiotic-synthesizing enzyme EpiD reveals a function for bacterial Dfp proteins in coenzyme A biosynthesis Authors: Kupke, T. / Uebele, M. / Schmid, D. / Jung, G. / Blaesse, M. / Steinbacher, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g63.cif.gz | 410.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g63.ent.gz | 338.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g63 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g63 | HTTPS FTP |
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-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: 20845.031 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: TUE3298 / Gene: EPID / Plasmid: PQE12 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P30197 #2: Chemical | ChemComp-FMN / #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: 2.89 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 100 mM MES/NaOH 30% MPD , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.09 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 25, 1998 / Details: Double focussing X-ray optics |
Radiation | Monochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 213488 / Num. obs: 213488 / % possible obs: 87.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 5.8 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.8 / Rsym value: 24.8 / % possible all: 73.3 |
Reflection | *PLUS Num. obs: 81936 / Num. measured all: 213488 |
Reflection shell | *PLUS % possible obs: 73.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→14.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2538485.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: maximum likelihood procedure
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.65 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.369 / % reflection Rfree: 5 % / Rfactor Rwork: 0.294 |