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- PDB-6cqc: RNase P protein from Thermotoga maritima in complex with 1-(4-Flu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cqc | ||||||
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Title | RNase P protein from Thermotoga maritima in complex with 1-(4-Fluorophenyl)-2-thiourea | ||||||
![]() | Ribonuclease P protein component | ||||||
![]() | RNA BINDING PROTEIN | ||||||
Function / homology | ![]() 3'-tRNA processing endoribonuclease activity / ribonuclease P complex / tRNA 3'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torres-Larios, A. / Madrigal-Carrillo, E.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of novel RNase P inhibitors via an activity-binding-structure pipeline Authors: Madrigal-Carrillo, E.A. / Diaz-Tufinio, C.A. / Santamaria-Suarez, H.A. / Arciniega-Castro, M. / Torres-Larios, 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 | ![]() | 290.8 KB | Display | ![]() |
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PDB format | ![]() | 241.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.2 KB | Display | ![]() |
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Full document | ![]() | 466.5 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nz0S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14363.003 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: rnpA, TM_1463 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-8P4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.21 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: P protein from T. maritima in 50 mM Tris-HCl pH 7.5, 0.2 mM EDTA was crystallized at 3 mg/mL in 12% PEG-1000, 100 mm sodium acetate pH 4.8 and 200 mM potassium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2011 / Details: mirrors |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→46.29 Å / Num. obs: 67977 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Χ2: 0.71 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2724 / CC1/2: 0.915 / Rpim(I) all: 0.195 / Rrim(I) all: 0.287 / Χ2: 0.58 / % possible all: 78.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NZ0 Resolution: 1.54→46.286 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.85 / 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: LAST / Resolution: 1.54→46.286 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: 6.7409 Å / Origin y: 13.3899 Å / Origin z: 16.142 Å
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Refinement TLS group | Selection details: all |