+Open data
-Basic information
Entry | Database: PDB / ID: 1hhf | ||||||||||||
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Title | Decaplanin second P6122-Form | ||||||||||||
Components | DECAPLANIN | ||||||||||||
Keywords | ANTIBIOTIC / GLYCOPEPTIDE | ||||||||||||
Function / homology | Decaplanin / 4-epi-vancosamine / PHOSPHATE ION / : Function and homology information | ||||||||||||
Biological species | UNCULTURED ACTINOMYCETE (environmental samples) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.47 Å | ||||||||||||
Authors | Lehmann, C. / Vertessy, L. / Sheldrick, G.M. / Dauter, Z. / Dauter, M. | ||||||||||||
Citation | Journal: Helv.Chim.Acta / Year: 2003 Title: Structures of Four Crystal Forms of Decaplanin Authors: Lehmann, C. / Debreczeni, J.E. / Bunkoczi, G. / Dauter, M. / Dauter, Z. / 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 | 1hhf.cif.gz | 36.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hhf.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hhf ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hhf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein/peptide , 1 types, 4 molecules ABCD
#1: Protein/peptide |
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-Sugars , 2 types, 8 molecules
#2: Polysaccharide | alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Details: DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED References: Decaplanin #3: Sugar | ChemComp-ERE / Type: L-saccharide, alpha linking, Glycopeptide / Class: Antibiotic / Mass: 161.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C7H15NO3 Details: DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED References: Decaplanin |
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-Non-polymers , 3 types, 100 molecules
#4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE. HERE, DECAPLANIN IS REPRESENTED BY GROUPING TOGETHER THE ...DECAPLANIN |
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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: 5.38 Å3/Da / Density % sol: 69.1 % / Description: SAS OF CHLORINE AT 1.5A |
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Crystal grow | pH: 8.5 / Details: 0.1M TRIS/HCL, PH=8.5, 2M NH4H2PO4, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
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: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→48.39 Å / Num. obs: 24558 / % possible obs: 99.1 % / Redundancy: 12 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.74 |
Reflection shell | Resolution: 1.47→1.6 Å / Redundancy: 11 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.96 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.47→48.39 Å / Num. parameters: 4895 / Num. restraintsaints: 7785 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 348 / Occupancy sum non hydrogen: 541.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→48.39 Å
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Refine LS restraints |
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