+Open data
-Basic information
Entry | Database: PDB / ID: 1hhu | |||||||||||||||
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Title | Balhimycin in complex with D-Ala-D-Ala | |||||||||||||||
Components | BALHIMYCIN | |||||||||||||||
Keywords | ANTIBIOTIC / GLYCOPEPTIDE / CELL WALL PEPTIDES | |||||||||||||||
Function / homology | Balhimycin / beta-D-glucopyranose / CITRIC ACID / D-ALANINE / Chem-DVC / : Function and homology information | |||||||||||||||
Biological species | AMYCOLATOPSIS SP. (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.89 Å | |||||||||||||||
Authors | Lehmann, C. / Bunkoczi, G. / Sheldrick, G.M. / Vertessy, L. | |||||||||||||||
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 | 1hhu.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hhu.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hhu_validation.pdf.gz | 510.6 KB | Display | wwPDB validaton report |
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Full document | 1hhu_full_validation.pdf.gz | 527.2 KB | Display | |
Data in XML | 1hhu_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1hhu_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hhu ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hhu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein/peptide , 1 types, 4 molecules ABCD
-Sugars , 2 types, 8 molecules
#2: Sugar | ChemComp-BGC / Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 180.156 Da / Num. of mol.: 4 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 #3: Sugar | ChemComp-DVC / ( Type: L-saccharide, alpha linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 177.198 Da / Num. of mol.: 4 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, 140 molecules
#4: Chemical | ChemComp-DAL / #5: Chemical | ChemComp-CIT / #6: Chemical | #7: 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: 2.14 Å3/Da / Density % sol: 22.4 % |
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Crystal grow | pH: 7 / Details: 1M CIT, PH =7, 25% MPD |
-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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→27.99 Å / Num. obs: 42306 / % possible obs: 99.4 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.0169 / Net I/σ(I): 38.76 |
Reflection shell | Resolution: 0.89→1 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.0339 / Mean I/σ(I) obs: 24.67 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 0.89→27.99 Å / Num. parameters: 6200 / Num. restraintsaints: 9467 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: FRIDEL OPPOSITES DURING REFINEMENT NOT MERGED
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Solvent computation | Solvent model: METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 28 / Occupancy sum hydrogen: 354.5 / Occupancy sum non hydrogen: 630.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→27.99 Å
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Refine LS restraints |
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