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Open data
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Basic information
Entry | Database: PDB / ID: 1qow | |||||||||
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Title | Mersacidin from Bacillus | |||||||||
![]() | MERSACIDIN | |||||||||
![]() | ANTIBIOTIC / LANTIBIOTIC / METHICILLIN RESISTANCE / THIOESTER / TYPE B LANTIBIOTIC / LANTHIONINE | |||||||||
Function / homology | Type 2 lantibiotic, leader peptide domain / killing of cells of another organism / defense response to bacterium / signaling receptor binding / Mersacidin / METHANOL / Lantibiotic mersacidin![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Schneider, T.R. / Kaercher, J. / Sheldrick, G.M. | |||||||||
![]() | ![]() Title: Ab initio structure determination of the lantibiotic mersacidin. Authors: Schneider, T.R. / Karcher, J. / Pohl, E. / Lubini, P. / Sheldrick, G.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461 KB | Display | ![]() |
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Full document | ![]() | 462.6 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | ![]() Details: MERSACIDIN IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AA AND THE FORMATION OF THIOETHER BONDS ...Details: MERSACIDIN IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AA AND THE FORMATION OF THIOETHER BONDS WITH CYSTEINE. THE CARBOXY-TERMINAL BETA-METHYLLANTHIONINE UNDERGOES DECARBOXYLATION. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS. THIS IS FOLLOWED BY MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED PRECURSOR. Source: (natural) ![]() ![]() #2: Chemical | ChemComp-MOH / #3: Water | ChemComp-HOH / | Compound details | MERSACIDIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE ...MERSACIDIN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.84 % | |||||||||||||||
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Crystal grow | Temperature: 294 K / Method: evaporation / pH: 7 Details: LYOPHILIZED MERSACIDIN WAS DISSOLVED TO SATURATION IN METHANOL. CRYSTALS GREW AT ROOM TEMPERATURE BY SLOW EVAPORATION OF METHANOL FROM A 1:1 MIXTURE OF THE SATURATED SOLUTION WITH BENZENE ...Details: LYOPHILIZED MERSACIDIN WAS DISSOLVED TO SATURATION IN METHANOL. CRYSTALS GREW AT ROOM TEMPERATURE BY SLOW EVAPORATION OF METHANOL FROM A 1:1 MIXTURE OF THE SATURATED SOLUTION WITH BENZENE AND REACHED A MAXIMUM SIZE OF 0.3 X 0.3 X 0.3 MM IN 10 DAYS., pH 7.00 | |||||||||||||||
Crystal grow | *PLUS Method: slow evaporation | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.865 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→39.9 Å / Num. obs: 33469 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.06→1.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3 / % possible all: 99.6 |
Reflection | *PLUS Num. all: 33485 / Num. measured all: 164063 |
Reflection shell | *PLUS Mean I/σ(I) obs: 3.4 |
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Processing
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Refinement | Method to determine structure: HALF-BAKED / Resolution: 1.06→40 Å / Num. parameters: 7438 / Num. restraintsaints: 10782 / Cross valid method: FREE R-VALUE / σ(F): 0 StereochEM target val spec case: SIMILARITY RESTRAINTS FOR NON-STANDARD RESIDUES AS IMPLEMENTED IN SHELXL97 Stereochemistry target values: ENGH AND HUBER Details: MEROHEDRAL TWINNING: THE CRYSTAL WAS MEROHEDRALLY TWINNED. THE EFFECT OF MEROHEDRAL WAS TAKEN INTO ACCOUNT EMPLOYING THE METHOD OF PRATT ET AL., J.CHEM.SOC.(A)(1971)2146-2151 AND JAMESON ET ...Details: MEROHEDRAL TWINNING: THE CRYSTAL WAS MEROHEDRALLY TWINNED. THE EFFECT OF MEROHEDRAL WAS TAKEN INTO ACCOUNT EMPLOYING THE METHOD OF PRATT ET AL., J.CHEM.SOC.(A)(1971)2146-2151 AND JAMESON ET AL., ACTA CRYST.B54 (1982)443-449 AS IMPLEMENTED IN SHELXL-97 USING THE TWIN MATRIX: (0 1 0 1 0 0 0 0 -1). THE SIX MOLECULES IN THE ASYMMETRIC UNIT ARE ARRANGED WITH APPROXIMATE 32 (D3) POINT GROUP SYMMETRY AND CAN BE DESCRIBED AS A DIMER OF TRIMERS. THE TWO FOLD AXIS RUNS ALONG THE SHORT DIAGONAL OF THE A*B* PLANE.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 719 / Occupancy sum non hydrogen: 826 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→40 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 4 / Rfactor obs: 0.134 / Rfactor Rwork: 0.1414 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.027 |