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Yorodumi- PDB-9c3d: Crystal structure of metallo-beta-lactamase superfamily protein C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c3d | ||||||
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Title | Crystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / metallo-beta-lacatamase / CcrA-like_MBL / antibiotic-resistance / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID | ||||||
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 | Dyadobacter fermentans DSM 18053 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans Authors: Kim, Y. / Maltseva, N. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c3d.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c3d.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 9c3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c3d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9c3d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9c3d_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 9c3d_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/9c3d ftp://data.pdbj.org/pub/pdb/validation_reports/c3/9c3d | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 24892.285 Da / Num. of mol.: 1 / Fragment: UNP residues 20-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dyadobacter fermentans DSM 18053 (bacteria) Gene: Dfer_1371 / Plasmid: pMGCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: C6W709, beta-lactamase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 18637 / % possible obs: 98.3 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.035 / Rrim(I) all: 0.124 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.159 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 827 / CC1/2: 0.6 / Rpim(I) all: 0.387 / Rrim(I) all: 1.227 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.2 Å / SU ML: 0.2618 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7503 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→47.2 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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