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- PDB-3zmh: 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: 3zmh | ||||||
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Title | Structure of E.coli rhomboid protease GlpG in complex with monobactam L62 | ||||||
![]() | RHOMBOID PROTEASE GLPG | ||||||
![]() | HYDROLASE / INTRA-MEMBRANE PROTEASE / ACYL ENZYME / BETA LACTAMS / ANITBIOTIC | ||||||
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 | ![]() | 54.9 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zmiC ![]() 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
-Protein / Sugars , 2 types, 7 molecules A![](data/chem/img/BNG.gif)
![](data/chem/img/BNG.gif)
#1: Protein | Mass: 20343.133 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 91-270 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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#4: Sugar | ChemComp-BNG / |
-Non-polymers , 4 types, 42 molecules ![](data/chem/img/L62.gif)
![](data/chem/img/78C.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/78C.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-L62 / | ||
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#3: Chemical | ChemComp-78C / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | CYCLOPENTY |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 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: 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9687 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→76.62 Å / Num. obs: 13547 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 34.18 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XOV Resolution: 2.3→76.622 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML Details: BNG 405 IS IN SPECIAL POSITION. L62 IS COVALENTLY LINKED TO S201. EXTERNAL RESTRAINTS USED BETWEEN C2 OF 401 AND CL 409. A RACEMIC MIXTURE OF L62 WAS USED IN THE SOAKS. NOTE THAT THE ...Details: BNG 405 IS IN SPECIAL POSITION. L62 IS COVALENTLY LINKED TO S201. EXTERNAL RESTRAINTS USED BETWEEN C2 OF 401 AND CL 409. A RACEMIC MIXTURE OF L62 WAS USED IN THE SOAKS. NOTE THAT THE EXTERNALLY BOUND BETA LACTAM HAS THE OPPOSITE CHIRALITY OF THE BETA LACTAM BOUND TO S201.
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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: 34.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→76.622 Å
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Refine LS restraints |
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LS refinement shell |
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