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Open data
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Basic information
Entry | Database: PDB / ID: 6d13 | ||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of E.coli RppH-DapF complex | ||||||||||||||||||||||||||||||||||||
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![]() | isomerase/hydrolase / RNA decay / DapF / RppH / isomerase-hydrolase complex | ||||||||||||||||||||||||||||||||||||
Function / homology | ![]() diaminopimelate epimerase / diaminopimelate epimerase activity / pyrophosphatase activity / lysine biosynthetic process via diaminopimelate / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||
![]() | Gao, A. / Serganov, A. | ||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF. Authors: Gao, A. / Vasilyev, N. / Luciano, D.J. / Levenson-Palmer, R. / Richards, J. / Marsiglia, W.M. / Traaseth, N.J. / Belasco, J.G. / Serganov, A. | ||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.3 KB | Display | ![]() |
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PDB format | ![]() | 151.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 439.7 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d1qC ![]() 6d1vC ![]() 4ijzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30332.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S88 / ExPEC / Gene: dapF, ECS88_4235 / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 20911.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S88 / ExPEC / Gene: rppH, nudH, ECS88_3125 / Production host: ![]() ![]() References: UniProt: B7MLH6, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
#3: Chemical | ChemComp-IOD / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.39 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 15% (v/v)PEG4,000, 0.1 M Tris-HCl, pH 8.0, and 0.2 M KI |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→77.25 Å / Num. obs: 13075 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 3.06→3.27 Å / Rmerge(I) obs: 1.076 / Num. unique obs: 2296 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IJZ Resolution: 3.06→19.991 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→19.991 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.484 Å / Origin y: 46.4308 Å / Origin z: 65.8566 Å
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Refinement TLS group | Selection details: all |