[English] 日本語
Yorodumi- PDB-7c1o: Crystal structure of Aquifex aeolicus Era Y63A bound to GDP.AlF4- -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c1o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Aquifex aeolicus Era Y63A bound to GDP.AlF4- | ||||||
Components | GTPase Era | ||||||
Keywords | HYDROLASE / HAS-GTPase | ||||||
Function / homology | Function and homology information ribosomal small subunit binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA binding / GTPase activity / GTP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å | ||||||
Authors | Batra, S. / Prakash, B. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: To be published Title: Crystal structure of Aquifex aeolicus Era Y63A bound to GDP.AlF4- Authors: Batra, S. / Prakash, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7c1o.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7c1o.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 7c1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c1o_validation.pdf.gz | 839.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7c1o_full_validation.pdf.gz | 839.8 KB | Display | |
Data in XML | 7c1o_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7c1o_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/7c1o ftp://data.pdbj.org/pub/pdb/validation_reports/c1/7c1o | HTTPS FTP |
-Related structure data
Related structure data | 3ievS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34729.980 Da / Num. of mol.: 1 / Fragment: GTP binding domain / Mutation: Y63A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: era, era1, aq_1994 / Plasmid: pBA1971 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: O67800 |
---|
-Non-polymers , 7 types, 100 molecules
#2: Chemical | ChemComp-ALF / |
---|---|
#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-TRS / |
#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-K / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.17 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 10 mg/ml protein with equal volume of 100 mM Bis-Tris, 200 mM Ammonium acetate, 18 % PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 3, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→46.52 Å / Num. obs: 17524 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 16.9 / Num. measured all: 135548 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IEV Resolution: 2.18→46.52 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.1 Å2 / Biso mean: 51.3725 Å2 / Biso min: 22.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→46.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|