+Open data
-Basic information
Entry | Database: PDB / ID: 4v1u | ||||||
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Title | Heterocyclase in complex with substrate and Cofactor | ||||||
Components |
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Keywords | HYDROLASE / HETEROCYCLASE / CYANOBACTINS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LYNGBYA AESTUARII (bacteria) UNCULTURED PROCHLORON SP. (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Koehnke, J. / Naismith, J.H. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2015 Title: Structural Analysis of Leader Peptide Binding Enables Leader-Free Cyanobactin Processing. Authors: Koehnke, J. / Mann, G. / Bent, A.F. / Ludewig, H. / Shirran, S. / Botting, C. / Lebl, T. / Houssen, W.E. / Jaspars, M. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v1u.cif.gz | 612 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v1u.ent.gz | 507.4 KB | Display | PDB format |
PDBx/mmJSON format | 4v1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v1u_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4v1u_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4v1u_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 4v1u_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v1u ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v1u | HTTPS FTP |
-Related structure data
Related structure data | 4v1tC 4v1vC 4bs9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 86145.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LYNGBYA AESTUARII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0YXD2 #2: Protein | Mass: 6999.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UNCULTURED PROCHLORON SP. (environmental samples) Strain: PROCHLORON SP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0MHA3*PLUS |
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-Non-polymers , 4 types, 27 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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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: 2.47 Å3/Da / Density % sol: 50.14 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→76.4 Å / Num. obs: 42149 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.86→2.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BS9 Resolution: 2.86→76.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 40.95 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→76.4 Å
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Refine LS restraints |
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