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Yorodumi- PDB-2vma: The three-dimensional structure of the cytoplasmic domains of Eps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vma | ||||||
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Title | The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae | ||||||
Components | GENERAL SECRETION PATHWAY PROTEIN F | ||||||
Keywords | TRANSPORT PROTEIN / TRANSMEMBRANE / INNER MEMBRANE / TYPE 2 SECRETION / T4PB / T2SS / VIBRIO / CHOLERA / MEMBRANE / TRANSPORT / PROTEIN SECRETION | ||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | VIBRIO CHOLERAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.9 Å | ||||||
Authors | Abendroth, J. / Korotkov, K.V. / Mitchell, D.D. / Kreger, A. / Hol, W.G.J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2009 Title: The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf from the Type 2 Secretion System of Vibrio Cholerae. Authors: Abendroth, J. / Mitchell, D.D. / Korotkov, K.V. / Johnson, T.L. / Kreger, A. / Sandkvist, M. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vma.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vma.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vma ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vma | HTTPS FTP |
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-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 domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.99988, 0.00497, -0.01461), Vector: |
-Components
#1: Protein | Mass: 14028.238 Da / Num. of mol.: 2 / Fragment: RESIDUES 56-170 Source method: isolated from a genetically manipulated source Details: RESIDUES 56-170, PLUS C-TERMINAL TEV- CLEAVABLE HIS6-TAG Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PACYC-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45780 #2: Chemical | #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | Sequence details | CYTOPLASMI | |
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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 Å3/Da / Density % sol: 38.08 % / Description: NONE |
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Crystal grow | pH: 7 Details: 1UL PROTEIN, 1UL RESERVOIR: 12.5% PEG 400, 200MM CAOAC2, 100MM MES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Oct 23, 2006 / Details: MIRRORS |
Radiation | Monochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.82 Å / Num. obs: 18609 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 12.11 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.9 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→46.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.078 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.32 Å
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Refine LS restraints |
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