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- PDB-6v5m: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v5m | ||||||
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Title | Crystal Structure of Metallo Beta Lactamase from Hirschia baltica in Complex with Succinate | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / metallo beta lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica in Complex with Succinate. Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.8 KB | Display | ![]() |
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PDB format | ![]() | 85.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 298.4 KB | Display | ![]() |
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Full document | ![]() | 298 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 5.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v54S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25523.830 Da / Num. of mol.: 1 / Mutation: A257T / Source method: obtained synthetically Source: (synth.) ![]() References: UniProt: C6XID6, beta-lactamase |
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-Non-polymers , 6 types, 207 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-BTB / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0 M Succinic acid pH 7.0;0.1 M Bis-Tris Propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 31, 2017 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 45429 / % possible obs: 99.7 % / Redundancy: 14.1 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.138 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2116 / CC1/2: 0.494 / Rsym value: 0.933 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6V54 Resolution: 1.5→40.31 Å / SU ML: 0.1475 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.6231
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40.31 Å
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Refine LS restraints |
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LS refinement shell |
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