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Yorodumi- PDB-3zmj: Structure of E.coli rhomboid protease GlpG in complex with monoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zmj | ||||||
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Title | Structure of E.coli rhomboid protease GlpG in complex with monobactam L61 | ||||||
Components | RHOMBOID PROTEASE GLPG | ||||||
Keywords | HYDROLASE / INTRA-MEMBRANE PROTEASE / ACYL ENZYME / BETA LACTAMS / ANITBIOTIC | ||||||
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: 2.3 Å | ||||||
Authors | Vinothkumar, K.R. / Pierrat, O. / Large, J.M. / Freeman, M. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure of Rhomboid Protease in Complex with Beta-Lactam Inhibitors Defines the S2' Cavity. Authors: Vinothkumar, K.R. / Pierrat, O.A. / Large, J.M. / Freeman, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zmj.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zmj.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 3zmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zmj_validation.pdf.gz | 844 KB | Display | wwPDB validaton report |
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Full document | 3zmj_full_validation.pdf.gz | 835.2 KB | Display | |
Data in XML | 3zmj_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 3zmj_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zmj ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zmj | HTTPS FTP |
-Related structure data
Related structure data | 3zmhC 3zmiC 3zotC 2xovS 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: 20214.020 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 92-270 Source method: isolated from a genetically manipulated source Details: THE BETA LACTAM RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 ON C2-O1 TO FORM A COVALENT BOND 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: Chemical | ChemComp-L61 / | ||||||
#3: Sugar | ChemComp-BNG / #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | ISOBUTYL(1-PHENYLBUT-3-EN-1-YL)CARBAMATE (L61): L61 IS COVALENTLY BONDED TO S201. BNG 404 IS IN ...ISOBUTYL(1-PHENYLBUT-3-EN-1-YL)CARBAMATE (L61): L61 IS COVALENTLY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65.6 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.75 M AMMONIUM CHLORIDE, 0.1M BIS-TRIS, PH 7.0, 298 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→53.24 Å / Num. obs: 13419 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XOV Resolution: 2.3→53.235 Å / SU ML: 0.28 / σ(F): 1.37 / Phase error: 23.18 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→53.235 Å
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Refine LS restraints |
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LS refinement shell |
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