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Yorodumi- PDB-2xtu: Structure of E.coli rhomboid protease GlpG active site mutant, S2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xtu | ||||||
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Title | Structure of E.coli rhomboid protease GlpG active site mutant, S201T in trigonal crystal form | ||||||
Components | RHOMBOID PROTEASE GLPG | ||||||
Keywords | HYDROLASE / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Vinothkumar, K.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structure of Rhomboid Protease in a Lipid Environment Authors: Vinothkumar, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xtu.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xtu.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xtu ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xtu | HTTPS FTP |
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-Related structure data
Related structure data | 2xtvC 3b45S 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: 20471.262 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 91-271 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease | ||||
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#2: Sugar | ChemComp-BNG / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.58 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.5M AMMONIUM CHLORIDE, 0.1M BIS-TRIS PH7.0, 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.53 Å / Num. obs: 25582 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 21.99 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B45 Resolution: 1.85→38.223 Å / SU ML: 0.18 / σ(F): 1.39 / Phase error: 17.19 / 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: 80.13 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→38.223 Å
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Refine LS restraints |
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LS refinement shell |
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