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Yorodumi- PDB-6u0z: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u0z | |||||||||
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Title | Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed penicillin G | |||||||||
Components | Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase) | |||||||||
Keywords | HYDROLASE / lactam antibiotics / penicillin G / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Kim, Y. / Maltseva, N. / Endres, M. / 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 the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed penicillin G. Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u0z.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u0z.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 6u0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u0z_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 6u0z_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 6u0z_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6u0z_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/6u0z ftp://data.pdbj.org/pub/pdb/validation_reports/u0/6u0z | HTTPS FTP |
-Related structure data
Related structure data | 6u0yS 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 29172.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase |
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#2: Polysaccharide |
-Non-polymers , 5 types, 228 molecules
#3: Chemical | ChemComp-SO4 / | ||||
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#4: Chemical | ChemComp-PEG / | ||||
#5: Chemical | #6: Chemical | ChemComp-PNK / ( | #7: Water | ChemComp-HOH / | |
-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: 2.67 Å3/Da / Density % sol: 53.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 38907 / % possible obs: 100 % / Redundancy: 20.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 44.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 16 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 4 / Num. unique obs: 1892 / CC1/2: 0.894 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 6U0Y Resolution: 1.65→34.3 Å / SU ML: 0.1575 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3477
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→34.3 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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