+Open data
-Basic information
Entry | Database: PDB / ID: 1qow | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mersacidin from Bacillus | |||||||||
Components | MERSACIDIN | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | BACILLUS SP. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / HALF-BAKED / Resolution: 1.06 Å | |||||||||
Authors | Schneider, T.R. / Kaercher, J. / Sheldrick, G.M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Ab initio structure determination of the lantibiotic mersacidin. Authors: Schneider, T.R. / Karcher, J. / Pohl, E. / Lubini, P. / Sheldrick, G.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qow.cif.gz | 54 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qow.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qow ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qow | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Type: Oligopeptide / Class: Antibiotic / Mass: 1834.256 Da / Num. of mol.: 6 / Source method: isolated from a natural source 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) BACILLUS SP. (bacteria) / Strain: HIL Y-85, 54728 / References: UniProt: P43683, Mersacidin #2: Chemical | ChemComp-MOH / #3: Water | ChemComp-HOH / | Compound details | MERSACIDIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE ...MERSACIDIN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.84 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.865 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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.
| |||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
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 |