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- PDB-3zmi: Structure of E.coli rhomboid protease GlpG in complex with monoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zmi | ||||||
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Title | Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 | ||||||
![]() | RHOMBOID PROTEASE GLPG | ||||||
![]() | HYDROLASE / INTRA-MEMBRANE PROTEASE / ACYL ENZYME / BETA LACTAMS / ANTIBIOTIC | ||||||
Function / homology | ![]() rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vinothkumar, K.R. / Pierrat, O.A. / Large, J.M. / Freeman, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.4 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zmhC ![]() 3zmjC ![]() 3zotC ![]() 2xovS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-L6C / | ||||
#3: Sugar | ChemComp-BNG / #4: Water | ChemComp-HOH / | Nonpolymer details | (3R)-3-(PHENOXYCAR | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.8 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M NACL, 0.1M BIS-TRIS, PH7.0, 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 11, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55.29 Å / Num. obs: 15423 / % possible obs: 99.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 43.23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XOV Resolution: 2.2→44.87 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 23.97 / Stereochemistry target values: ML Details: RESIDUES 245-249 ARE DISORDERED. BNG 407 IS IN A SPECIAL POSITION AND REFINED WITH 0.5 OCCUPANCY.
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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: 46.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→44.87 Å
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Refine LS restraints |
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LS refinement shell |
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