+Open data
-Basic information
Entry | Database: PDB / ID: 8acu | ||||||
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Title | Structure of Bacillus subtilis Rel in complex with DarB | ||||||
Components |
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Keywords | TRANSFERASE / Rel / GTP pyrophosphokinase / DarB / CBPB / stringent factor / translation / ribosome | ||||||
Function / homology | Function and homology information GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å | ||||||
Authors | Garcia-Pino, A. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Structure of Bacillus subtilis Rel in complex with DarB Authors: Garcia-Pino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8acu.cif.gz | 380.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8acu.ent.gz | 309.7 KB | Display | PDB format |
PDBx/mmJSON format | 8acu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/8acu ftp://data.pdbj.org/pub/pdb/validation_reports/ac/8acu | HTTPS FTP |
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-Related structure data
Related structure data | 6s2tS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43479.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: relA, BSU27600 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O54408, GTP diphosphokinase #2: Protein | Mass: 16653.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3749, Bateq7PJ16_1575, C6Y43_13715, FAL52_03995 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A164SLA6 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 293.16 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Magnesium chloride hexahydrate 0.1 M Sodium HEPES 7.5 10 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→77.6 Å / Num. obs: 22489 / % possible obs: 95 % / Redundancy: 20.1 % / CC1/2: 0.998 / Rpim(I) all: 0.061 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.97→3.08 Å / Num. unique obs: 1023 / CC1/2: 0.387 / Rpim(I) all: 0.851 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S2T Resolution: 2.97→75.72 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.52 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.97→75.72 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: 16.9521 Å / Origin y: -24.4312 Å / Origin z: 27.0744 Å
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Refinement TLS group | Selection details: all |