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Open data
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Basic information
Entry | Database: PDB / ID: 3id2 | ||||||
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Title | Crystal Structure of RseP PDZ2 domain | ||||||
![]() | Regulator of sigma E protease | ||||||
![]() | HYDROLASE / Cell inner membrane / Cell membrane / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane / Zinc | ||||||
Function / homology | ![]() anti-sigma factor antagonist activity / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / cellular response to cell envelope stress / metalloendopeptidase activity / positive regulation of DNA-templated transcription / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X. / Wang, B. / Feng, L. / Wang, J. / Shi, Y. | ||||||
![]() | ![]() Title: Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage Authors: Li, X. / Wang, B. / Feng, L. / Kang, H. / Qi, Y. / Wang, J. / Shi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.4 KB | Display | ![]() |
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PDB format | ![]() | 63.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3id1C ![]() 3id3C ![]() 3id4C ![]() 2zpmS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 9608.105 Da / Num. of mol.: 2 / Fragment: PDZ2 domain, residues 222-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AEH1, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-IOD / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4M Sodium Formate, 4% Methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.089→39.82 Å / Num. obs: 6668 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 67.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 3.089→3.2 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.24 / Num. unique all: 6696 / Rsym value: 0.393 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZPM Resolution: 3.089→39.817 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.805 / SU ML: 0.5 / Isotropic thermal model: Isotropic / σ(F): 0.01 / Phase error: 25.94 / 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 / Bsol: 63.998 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 212.29 Å2 / Biso mean: 69.08 Å2 / Biso min: 11.79 Å2
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Refinement step | Cycle: LAST / Resolution: 3.089→39.817 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | S31: -0.1667 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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