+Open data
-Basic information
Entry | Database: PDB / ID: 3id1 | ||||||
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Title | Crystal Structure of RseP PDZ1 domain | ||||||
Components | Regulator of sigma E protease | ||||||
Keywords | HYDROLASE / Cell inner membrane / Cell membrane / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane / Zinc | ||||||
Function / homology | Function and homology information 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 | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.67 Å | ||||||
Authors | Li, X. / Wang, B. / Feng, L. / Wang, J. / Shi, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3id1.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3id1.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 3id1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3id1_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
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Full document | 3id1_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 3id1_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3id1_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3id1 ftp://data.pdbj.org/pub/pdb/validation_reports/id/3id1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10315.558 Da / Num. of mol.: 1 / Fragment: PDZ1 domain, residues 127-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rseP / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0AEH1, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Bis-tris propane, pH7.0, 2.5M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 5, 2008 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→30 Å / Num. obs: 14152 / % possible obs: 93.1 % / Redundancy: 5.91 % / Biso Wilson estimate: 17.77 Å2 / Rsym value: 0.035 / Net I/σ(I): 26.9 / Num. measured all: 89799 |
Reflection shell | Resolution: 1.67→1.77 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1808 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.67→29.87 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.843 / SU ML: 0.26 / Isotropic thermal model: isotropic / σ(F): 0.08 / σ(I): 3.2 / Phase error: 22.38 / 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: 62.528 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.45 Å2 / Biso mean: 30.078 Å2 / Biso min: 9.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→29.87 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: 24.2485 Å / Origin y: -12.6654 Å / Origin z: 1.6656 Å
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Refinement TLS group | Selection details: chain A |