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Yorodumi- PDB-4pm3: Structure of the double-stranded DNA binding type IV secretion pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pm3 | |||||||||
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Title | Structure of the double-stranded DNA binding type IV secretion protein TraN from Enterococcus | |||||||||
Components | AM32 | |||||||||
Keywords | DNA BINDING PROTEIN / Type IV secretion / internal dimer / isomerase | |||||||||
Function / homology | isomerase activity / BROMIDE ION / : / AM32 Function and homology information | |||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | |||||||||
Model details | helix-turn-helix-like motif, beta-barrel-like motif | |||||||||
Authors | Goessweiner-Mohr, N. / Keller, W. | |||||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2014 Title: Structure of the double-stranded DNA binding type IV secretion protein TraN from Enterococcus Authors: Goessweiner-Mohr, N. / Eder, M. / Hofer, G. / Fercher, C. / Arends, K. / Birner-Gruenberger, R. / Grohmann, E. / Keller, W. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2012 Title: Crystallization and first data collection of the putative transfer protein TraN from Gram-positive conjugative plasmid pIP501 Authors: Goessweiner-Mohr, N. / Fercher, C. / Abajy, M.Y. / Grohmann, E. / Keller, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pm3.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pm3.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pm3 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pm3 | HTTPS FTP |
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-Related structure data
Related structure data | 4p0yC 4p0zSC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological unit is a monomer. There are two biological units present in the asymmetric unit (chain A, chain B). |
-Components
#1: Protein | Mass: 17599.949 Da / Num. of mol.: 2 / Fragment: TraN Source method: isolated from a genetically manipulated source Details: MKHHHHHHHSDYDIPTTENLYFQGSGS is the 7x N-terminal HisTag HisTag and several N-terminal and C-terminal residues are not visible in the density map. Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BVV5 #2: Chemical | #3: Chemical | ChemComp-BR / #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: 1.93 Å3/Da / Density % sol: 36.16 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 5.5 Details: 1:1 setup of purification buffer with Index screen condition 42 (0.1 M Bis-Tris, 25.0 % PEG 3350); final protein concentration: 3.25 mg/ml Crystal soaked for 1.5 h with Br4Pt |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Pt LIII high-end remote | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0615 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2010 Details: toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: BARTELS MONOCROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0615 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.6 % / Number: 69059 / Rsym value: 0.12 / D res high: 1.8 Å / D res low: 57.679 Å / Num. obs: 19191 / % possible obs: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.8→57.68 Å / Num. all: 19191 / Num. obs: 19191 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.79 Å2 / Rpim(I) all: 0.073 / Rrim(I) all: 0.141 / Rsym value: 0.12 / Net I/av σ(I): 4.67 / Net I/σ(I): 8.8 / Num. measured all: 69059 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P0Z Resolution: 1.8→28.967 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→28.967 Å
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Refine LS restraints |
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LS refinement shell |
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