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Yorodumi- PDB-6v70: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v70 | ||||||
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Title | Crystal Structure of Metallo Beta Lactamase from Hirschia baltica with Cadmium in the Active Site | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Hirschia baltica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica. Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v70.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v70.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v70_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 6v70_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6v70_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 6v70_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/6v70 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v70 | HTTPS FTP |
-Related structure data
Related structure data | 6v54SC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25852.098 Da / Num. of mol.: 1 / Mutation: A257T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418) (bacteria) Strain: ATCC 49814 / DSM 5838 / IFAM 1418 / Gene: Hbal_3075 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: C6XID6, beta-lactamase |
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-Non-polymers , 5 types, 116 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 8000; 0.1M TRIS pH 8.5; 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 22753 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 33.79 Å2 / Rsym value: 0.091 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.95→1.98 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 1121 / CC1/2: 0.658 / Rsym value: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6V54 Resolution: 1.95→33.47 Å / SU ML: 0.1972 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.5337
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→33.47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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