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Yorodumi- PDB-3wkm: The periplasmic PDZ tandem fragment of the RseP homologue from Aq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wkm | ||||||
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Title | The periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus in complex with the Fab fragment | ||||||
Components |
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Keywords | HYDROLASE / PDZ DOMAIN | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nogi, T. / Tabata, S. / Tamura-kawakami, K. / Takagi, J. | ||||||
Citation | Journal: Structure / Year: 2013 Title: A Structure-Based Model of Substrate Discrimination by a Noncanonical PDZ Tandem in the Intramembrane-Cleaving Protease RseP Authors: Hizukuri, Y. / Oda, T. / Tabata, S. / Tamura-kawakami, K. / Oi, R. / Sato, M. / Takagi, J. / Akiyama, Y. / Nogi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wkm.cif.gz | 250.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wkm.ent.gz | 199.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wkm_validation.pdf.gz | 466.3 KB | Display | wwPDB validaton report |
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Full document | 3wkm_full_validation.pdf.gz | 483.7 KB | Display | |
Data in XML | 3wkm_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 3wkm_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkm ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkm | HTTPS FTP |
-Related structure data
Related structure data | 3wklC 1nsnS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19997.455 Da / Num. of mol.: 2 / Fragment: PDZ TANDEM FRAGMENT, UNP RESIDUES 115-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1964 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O67776, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Antibody | Mass: 24268.041 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) #3: Antibody | Mass: 24080.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) #4: Water | ChemComp-HOH / | Sequence details | DNA SEQUENCEs FOR CHAIN H, I, L AND M WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ...DNA SEQUENCEs FOR CHAIN H, I, L AND M WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | pH: 7 Details: 16%(W/V) POLYETHYLENE GLYCOL 8000, 200MM SODIUM MALONATE, 0.5%(W/) N-OCTYL BETA-D-GLUCOPYRANOSIDE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.44 Å / Num. obs: 74923 / % possible obs: 98.2 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NSN Resolution: 2.2→47.44 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.989 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→47.44 Å
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Refine LS restraints |
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