+Open data
-Basic information
Entry | Database: PDB / ID: 3o1f | ||||||
---|---|---|---|---|---|---|---|
Title | P1 crystal form of E. coli ClpS at 1.4 A resolution | ||||||
Components | (ATP-dependent Clp protease adapter protein clpS) x 2 | ||||||
Keywords | HYDROLASE / adaptor | ||||||
Function / homology | Function and homology information molecular function inhibitor activity / protein catabolic process / peptidase activity / protein-folding chaperone binding / response to heat / proteolysis Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Roman-Hernandez, G. / Hou, J.Y. / Grant, R.A. / Sauer, R.T. / Baker, T.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: The ClpS Adaptor Mediates Staged Delivery of N-End Rule Substrates to the AAA+ ClpAP Protease. Authors: Roman-Hernandez, G. / Hou, J.Y. / Grant, R.A. / Sauer, R.T. / Baker, T.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3o1f.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3o1f.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 3o1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/3o1f ftp://data.pdbj.org/pub/pdb/validation_reports/o1/3o1f | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9305.767 Da / Num. of mol.: 1 / Fragment: unp residues 26-106 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpS / Production host: Escherichia coli (E. coli) / References: UniProt: D3QP81, UniProt: P0A8Q6*PLUS |
---|---|
#2: Protein | Mass: 9289.767 Da / Num. of mol.: 1 / Fragment: unp residues 26-106 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpS / Production host: Escherichia coli (E. coli) / References: UniProt: D3QP81, UniProt: P0A8Q6*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.13 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M Ammonium Formate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 19, 2010 / Details: Varimax-HR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax-HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→50 Å / Num. all: 23654 / Num. obs: 23654 / % possible obs: 82.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.036 / Χ2: 1.003 / Net I/σ(I): 17.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→22.488 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8593 / SU ML: 0.22 / σ(F): 2.03 / Phase error: 21.39 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.018 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.12 Å2 / Biso mean: 17.85 Å2 / Biso min: 6.72 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→22.488 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|