+Open data
-Basic information
Entry | Database: PDB / ID: 1go6 | |||||||||
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Title | Balhimycin in complex with Lys-D-ala-D-ala | |||||||||
Components |
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Keywords | ANTIBIOTIC/PEPTIDE / GLYCOPEPTIDE / ANTIBIOTICS / ANTIBIOTIC-PEPTIDE COMPLEX / BACTERIAL CELL-WALL | |||||||||
Function / homology | Balhimycin / beta-D-glucopyranose / CITRIC ACID / Chem-DVC / : Function and homology information | |||||||||
Biological species | AMYCOLATOPSIS SP. (bacteria) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.98 Å | |||||||||
Authors | Lehmann, C. / Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structures of Glycopeptide Antibiotics with Peptides that Model Bacterial Cell-Wall Precursors Authors: Lehmann, C. / 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 | 1go6.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1go6.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1go6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1go6_validation.pdf.gz | 492.8 KB | Display | wwPDB validaton report |
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Full document | 1go6_full_validation.pdf.gz | 530.4 KB | Display | |
Data in XML | 1go6_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1go6_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/1go6 ftp://data.pdbj.org/pub/pdb/validation_reports/go/1go6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein/peptide , 2 types, 12 molecules ACEGIKMOBDFH
-Sugars , 2 types, 16 molecules
#3: Sugar | ChemComp-BGC / Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 180.156 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Formula: C6H12O6 Details: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4 AND BY 4-OXO-VANCOSAMINE (RESIDUE 9) ON RESIDUE 6. References: Balhimycin #4: Sugar | ChemComp-DVC / ( Type: L-saccharide, alpha linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 177.198 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Formula: C7H15NO4 Details: BALHIMYCIN IS A TRICYCLIC HEPTAPEPTIDE GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4 AND BY 4-OXO-VANCOSAMINE (RESIDUE 9) ON RESIDUE 6. References: Balhimycin |
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-Non-polymers , 4 types, 266 molecules
#5: Chemical | ChemComp-CIT / #6: Chemical | ChemComp-MRD / ( | #7: Chemical | ChemComp-MPD / ( | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | BALHIMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...BALHIMYCIN |
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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: 2.9 Å3/Da / Density % sol: 57.6 % Description: ADDITIONAL DATA SET WAS COLLECTED AT CU KALPHA RADIATION | ||||||||||||||||||||
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Crystal grow | pH: 4 / Details: 0.3 M NA3CIT/H3CIT PH=4, 25% MPD, pH 4.00 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 4 / Method: vapor diffusion, hanging drop / Details: Loll, P.J., (1999) J.Med.Chem., 42, 4714. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→90 Å / Num. obs: 72913 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.81 |
Reflection shell | Resolution: 0.98→1.1 Å / Rmerge(I) obs: 0.1774 / Mean I/σ(I) obs: 6.72 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 90 Å / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS Lowest resolution: 1.1 Å / % possible obs: 95.5 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.98→89 Å / Num. parameters: 12104 / Num. restraintsaints: 16491 / Cross valid method: FREE R-VALUE / σ(F): 0 StereochEM target val spec case: RESTRAINTS FOR BALHIMYCIN FROM CSD Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 728.86 / Occupancy sum non hydrogen: 1106.67 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→89 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1254 / Rfactor Rfree: 0.1542 / Rfactor Rwork: 0.1254 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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