+Open data
-Basic information
Entry | Database: PDB / ID: 5amu | ||||||
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Title | IglE I39A,Y40A,V44A | ||||||
Components | IGLE | ||||||
Keywords | UNKNOWN FUNCTION / TYPE SIX SECRETION SYSTEM / LIPOPROTEIN | ||||||
Function / homology | symbiont cell surface / Prokaryotic membrane lipoprotein lipid attachment site profile. / host cell cytoplasm / Lipoprotein Function and homology information | ||||||
Biological species | FRANCISELLA NOVICIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Robb, C.S. / Nano, F.E. / Boraston, A.B. | ||||||
Citation | Journal: To be Published Title: The Structure, Dimerisation and Impact on Intramacrophage Replication of Igle in Francisella Novicida Authors: Robb, C.S. / Nano, F.E. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5amu.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amu.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 5amu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5amu_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 5amu_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 5amu_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 5amu_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amu ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amu | HTTPS FTP |
-Related structure data
Related structure data | 5amtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.027 Da / Num. of mol.: 2 / Fragment: UNIPROT RESIDUES 25-125 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) FRANCISELLA NOVICIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0Q7H2 #2: 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: 1.79 Å3/Da / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22.07 Å / Num. obs: 10932 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5AMT Resolution: 2.2→21.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.659 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.235 / 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: 29.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→21.82 Å
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Refine LS restraints |
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