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Yorodumi- PDB-7uhs: SSX Structure of Metallo Beta-Lactamase L1 with Two Water Molecul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uhs | ||||||
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Title | SSX Structure of Metallo Beta-Lactamase L1 with Two Water Molecules in the Active Site | ||||||
Components | Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase) | ||||||
Keywords | HYDROLASE / metallo beta lactamase / moxalactam / serial crystallography / 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 K279a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Henning, R. / Maltseva, N. / Endres, M. / Babnigg, G. / Srajer, V. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase. Authors: Wilamowski, M. / Sherrell, D.A. / Kim, Y. / Lavens, A. / Henning, R.W. / Lazarski, K. / Shigemoto, A. / Endres, M. / Maltseva, N. / Babnigg, G. / Burdette, S.C. / Srajer, V. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uhs.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uhs.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 7uhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uhs_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 7uhs_full_validation.pdf.gz | 426.8 KB | Display | |
Data in XML | 7uhs_validation.xml.gz | 11 KB | Display | |
Data in CIF | 7uhs_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/7uhs ftp://data.pdbj.org/pub/pdb/validation_reports/uh/7uhs | HTTPS FTP |
-Related structure data
Related structure data | 7l91C 7uhhC 7uhiC 7uhjC 7uhkC 7uhlC 7uhmC 7uhnC 7uhoC 7uhpC 7uhqC 7uhrC 7uhtC 7l52S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29243.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria) Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B2FTM1, beta-lactamase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow | Temperature: 289 K / Method: batch mode Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate ...Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350. |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.8 Å / Num. obs: 17385 / % possible obs: 100 % / Redundancy: 76.5 % / Biso Wilson estimate: 34.26 Å2 / CC1/2: 0.95 / R split: 0.25 / Net I/σ(I): 2.51 |
Reflection shell | Resolution: 2.2→2.24 Å / Num. unique obs: 865 / CC1/2: 0.41 / % possible all: 100 |
Serial crystallography sample delivery | Description: Nylon Mesh / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: ALEX mesh holder Motion control: SmarAct Motors viaPMAC start/stop raster over area Sample holding: nylon mesh / Support base: xyz stage |
Serial crystallography data reduction | Crystal hits: 5191 / Frames indexed: 4550 / Frames total: 38500 / Lattices indexed: 4550 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7L52 Resolution: 2.2→46.8 Å / SU ML: 0.3157 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6289 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 45.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.8 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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