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Yorodumi- PDB-2jgp: Structure of the TycC5-6 PCP-C bidomain of the tyrocidine synthet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jgp | ||||||
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Title | Structure of the TycC5-6 PCP-C bidomain of the tyrocidine synthetase TycC | ||||||
Components | TYROCIDINE SYNTHETASE 3 | ||||||
Keywords | LIGASE / MULTIFUNCTIONAL ENZYME / ANTIBIOTIC BIOSYNTHESIS / CONDENSATION DOMAIN / PEPTIDE BOND FORMATION / TYROCIDINE / ANTIBIOTICS / PHOSPHOPANTETHEINE / NONRIBOSOMAL PEPTIDE SYNTHETASE / PEPTIDYL CARRIER DOMAIN | ||||||
Function / homology | Function and homology information amide biosynthetic process / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Samel, S.A. / Schoenafinger, G. / Knappe, T.A. / Marahiel, M.A. / Essen, L.-O. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Structural and Functional Insights Into a Peptide Bond-Forming Bidomain from a Nonribosomal Peptide Synthetase. Authors: Samel, S.A. / Schoenafinger, G. / Knappe, T.A. / Marahiel, M.A. / Essen, L.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jgp.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgp.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgp ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgp | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58904.402 Da / Num. of mol.: 1 Fragment: PCP-C BIDOMAIN OF TYCC MODULE 5 AND 6, RESIDUES 5116-5633 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BREVIBACILLUS BREVIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: O30409 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 42.5 % Description: SEMET DATA COLLECTED FOR MAD STRUCTURE DETERMINATION |
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Crystal grow | pH: 6.5 Details: 7.5 MG PROTEIN/ML MIXED 1:1 WITH A RESERVOIR SOLUTION CONTAINING 1.6 M AMMONIUM SULFATE, 0.04 M MES (PH 6.5) AND 4% DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.808 |
Detector | Type: MAR / Detector: CCD / Date: Jun 1, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 51834 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.05 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.85→19.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.329 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DISORDERED REGION T456-G460 WAS MODELED STEREOCHEMICALLY IN VERY WEAK DIFFERENCE ELECTRON DENSITY, BUT ITS OCCUPANCY WAS SET TO ZERO.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.81 Å
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Refine LS restraints |
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