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Yorodumi- PDB-4uhv: The structure of VgrG1, the needle tip of the bacterial Type VI S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uhv | ||||||
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Title | The structure of VgrG1, the needle tip of the bacterial Type VI Secretion System | ||||||
Components | VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1 | ||||||
Keywords | STRUCTURAL PROTEIN / VGRG1 / VIRULENCE / TOXIN / EFFECTOR / PUNCTURING DEVICE / SPIKE / T6SS / P. AERUGINOSA | ||||||
Function / homology | Function and homology information type VI protein secretion system complex / protein secretion by the type VI secretion system / extracellular region Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Spinola-Amilibia, M. / Davo-Siguero, I. / Ruiz, F.M. / Santillana, E. / Medrano, F.J. / Romero, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: The Structure of Vgrg1 from Pseudomonas Aeruginosa, the Needle Tip of the Bacterial Type Vi Secretion System Authors: Spinola-Amilibia, M. / Davo-Siguero, I. / Ruiz, F.M. / Santillana, E. / Medrano, F.J. / Romero, A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uhv.cif.gz | 278.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uhv.ent.gz | 226.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/4uhv ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uhv | HTTPS FTP |
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-Related structure data
Related structure data | 4mtkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 73591.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET29_VGRG1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q9I741 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / #4: 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: 2.62 Å3/Da / Density % sol: 53.1 % / Description: TWINNED DATA, L-TEST OF 0.34 |
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Crystal grow | pH: 7.2 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M HEPES PH 7.2, 0.2 M LITHIUM SULPHATE AND 38 % MPD; THEN THE CRYSTAL WAS SOAKED IN 2 MM NEODYMIUM (III) SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.72785 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014 / Details: KB MIRRORS | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.72785 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.88→86.06 Å / Num. obs: 111022 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 6 | |||||||||||||||
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.1 / % possible all: 56.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4MTK Resolution: 2→71.73 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU B: 3.812 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 36.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2→71.73 Å
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Refine LS restraints |
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