+Open data
-Basic information
Entry | Database: PDB / ID: 1w3m | ||||||
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Title | Crystal structure of tsushimycin | ||||||
Components | TSUSHIMYCIN | ||||||
Keywords | ANTIBIOTIC / AMPHOMYCIN / DAPTOMYCIN / LIPOPETIDE / ANTIBACTERIAL | ||||||
Function / homology | Tsushimycin / ETHANOL / Delta-3isotetradecenoic acid / : Function and homology information | ||||||
Biological species | ACTINOPLANES FRIULIENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1 Å | ||||||
Authors | Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005 Title: Structure of the lipopeptide antibiotic tsushimycin. Authors: Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w3m.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w3m.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w3m_validation.pdf.gz | 536.6 KB | Display | wwPDB validaton report |
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Full document | 1w3m_full_validation.pdf.gz | 550 KB | Display | |
Data in XML | 1w3m_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1w3m_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w3m ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w3m | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein/peptide , 1 types, 12 molecules ABCDEFGHIJKL
-Non-polymers , 5 types, 255 molecules ABCDEFGHIJKL
#2: Chemical | ChemComp-LNG / Type: Lipopeptide / Class: Antibiotic / Mass: 226.355 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H26O2 Details: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ...Details: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ACID IS LINKED TO THE RESIDUE 1 References: Tsushimycin #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EOH / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | TSUSHIMYCIN IS A CYCLIC DODEDECAMER LIPOPETIDE. HERE, TSUSHIMYCIN IS REPRESENTED BY GROUPING ...TSUSHIMYCI |
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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: 2.41 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1 M NAAC/HAC PH=4.0 0.12 M HAC 38% ETOH 0.80 M CACL2 0.40 M 1,6-HEXANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 12, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1→26.02 Å / Num. obs: 355145 / % possible obs: 96.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.49 |
Reflection shell | Resolution: 1→1.1 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.35 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1→99 Å / Num. parameters: 11896 / Num. restraintsaints: 14162 / Cross valid method: FREE R-VALUE / σ(F): 0 Stereochemistry target values: ENGH AND HUBER GENERATED USING CCDC
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Refine analyze | Num. disordered residues: 26 / Occupancy sum hydrogen: 829 / Occupancy sum non hydrogen: 1259.82 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→99 Å
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Refine LS restraints |
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