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Yorodumi- PDB-5g5x: CBS domain tandem of site-2 protease from Archaeoglobus fulgidus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g5x | ||||||
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Title | CBS domain tandem of site-2 protease from Archaeoglobus fulgidus in complex with llama Nanobody - nucleotide-bound form | ||||||
Components |
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Keywords | HYDROLASE / METALLOPROTEASE / SITE-2 PROTEASE / REGULATORY DOMAIN / NUCLEOTIDE-BINDING / CBS DOMAIN / CAMELID ANTIBODY / NANOBODY | ||||||
Function / homology | Function and homology information metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) LAMA GLAMA (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Schacherl, M. / Baumann, U. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease. Authors: Schacherl, M. / Gompert, M. / Pardon, E. / Lamkemeyer, T. / Steyaert, J. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g5x.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5x.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 5g5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5x ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5x | HTTPS FTP |
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-Related structure data
Related structure data | 5g5rSC S: Starting model for refinement C: citing same article (ref.) |
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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: 15469.021 Da / Num. of mol.: 1 / Fragment: REGULATORY DOMAIN, RESIDUES 236-362 Source method: isolated from a genetically manipulated source Details: C-TERMINAL STREPII-TAG / Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: DSM 4304 GENOMIC DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O29915, EC: 3.4.24.85 |
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#2: Antibody | Mass: 13318.636 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NB330, SELECTED FROM LLAMA, C-TERMINAL 6XHIS- TAG / Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PHEN6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): WK6 |
#3: Chemical | ChemComp-AMP / |
#4: Chemical | ChemComp-ATP / |
Sequence details | D236-S362 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M IMIDAZOLE PH 7.25, 0.2 M MGCL2, 12 % ETHANOL |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→61.41 Å / Num. obs: 7966 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9.58 % / Biso Wilson estimate: 72.63 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.21 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 9.27 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.16 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5G5R Resolution: 2.8→52.433 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 31.71 / 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: 61.8 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→52.433 Å
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Refine LS restraints |
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LS refinement shell |
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