+Open data
-Basic information
Entry | Database: PDB / ID: 3id4 | ||||||
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Title | Crystal Structure of RseP PDZ2 domain fused GKASPV peptide | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 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 | 3id4.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3id4.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 3id4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3id4_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
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Full document | 3id4_full_validation.pdf.gz | 420.9 KB | Display | |
Data in XML | 3id4_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 3id4_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3id4 ftp://data.pdbj.org/pub/pdb/validation_reports/id/3id4 | HTTPS FTP |
-Related structure data
Related structure data | 3id1C 3id2SC 3id3C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9798.302 Da / Num. of mol.: 1 / Fragment: PDZ2 domain, residues 222-307 Source method: isolated from a genetically manipulated source Details: Carboxy-terminally fused GKASPV peptide / 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 / |
Sequence details | THE FUSED PEPTIDE OF GLY308 TO VAL313 IS CARBOXT-TERMINUS OF RSEA BY DEGS CLEAVAGE. THE DEPOSITORS ...THE FUSED PEPTIDE OF GLY308 TO VAL313 IS CARBOXT-TERMINUS OF RSEA BY DEGS CLEAVAGE. THE DEPOSITORS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M (NH4)2SO4, 30%(w/v) Polyethylene Glycol 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.96386 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96386 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 10945 / % possible obs: 97.5 % / Redundancy: 3 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.06 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 469 / Rsym value: 0.246 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ID2 Resolution: 1.604→21.766 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.849 / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 0.09 / Phase error: 22.61 / 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: 56.077 Å2 / ksol: 0.405 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.79 Å2 / Biso mean: 30.269 Å2 / Biso min: 12.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.604→21.766 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. | Method: refined / Origin x: 3.0364 Å / Origin y: 6.5931 Å / Origin z: 8.3741 Å
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Refinement TLS group | Selection details: chain A |