+Open data
-Basic information
Entry | Database: PDB / ID: 4tx2 | |||||||||
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Title | Crystal structure of the X-domain from teicoplanin biosynthesis | |||||||||
Components | Non-ribosomal peptide synthetase | |||||||||
Keywords | PROTEIN BINDING / non-ribosomal peptide synthetase / condensation type domain / teicoplanin biosynthesis / oxygenase complex | |||||||||
Function / homology | Function and homology information amide biosynthetic process / : / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity Similarity search - Function | |||||||||
Biological species | Actinoplanes teichomyceticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Peschke, M. / Haslinger, K. / Cryle, M.J. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Nature / Year: 2015 Title: X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis. Authors: Haslinger, K. / Peschke, M. / Brieke, C. / Maximowitsch, E. / Cryle, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tx2.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tx2.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 4tx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tx2_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 4tx2_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 4tx2_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4tx2_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/4tx2 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4tx2 | HTTPS FTP |
-Related structure data
Related structure data | 4tx3C 2jgpS 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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Unit cell |
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-Components
#1: Protein | Mass: 53435.977 Da / Num. of mol.: 1 / Fragment: UNP residues 1047-1511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: tcp12 / Plasmid: pET24d / Details (production host): GB1 fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AZ6 |
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#2: 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: 2.68 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Bis-Tris, 200 mM (NH4)2SO4, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→48 Å / Num. obs: 12768 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.5 % / Biso Wilson estimate: 42.4 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.122 / Χ2: 0.914 / Net I/σ(I): 24.31 / Num. measured all: 261201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JGP Resolution: 2.9→44.186 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.88 Å2 / Biso mean: 30.6939 Å2 / Biso min: 3.42 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→44.186 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %
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