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Yorodumi- PDB-4qd4: Structure of ADC-68, a Novel Carbapenem-Hydrolyzing Class C Exten... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qd4 | ||||||
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Title | Structure of ADC-68, a Novel Carbapenem-Hydrolyzing Class C Extended-Spectrum -Lactamase from Acinetobacter baumannii | ||||||
Components | Beta-lactamase ADC-68 | ||||||
Keywords | HYDROLASE / Beta-lactamase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hong, M.K. / Kang, L.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of ADC-68, a novel carbapenem-hydrolyzing class C extended-spectrum beta-lactamase isolated from Acinetobacter baumannii Authors: Jeon, J.H. / Hong, M.K. / Lee, J.H. / Lee, J.J. / Park, K.S. / Karim, A.M. / Jo, J.Y. / Kim, J.H. / Ko, K.S. / Kang, L.W. / Lee, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qd4.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qd4.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qd4_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 4qd4_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 4qd4_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 4qd4_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/4qd4 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/4qd4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40692.426 Da / Num. of mol.: 2 / Fragment: UNP residues 24-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaADC-68 / Production host: Escherichia coli (E. coli) / References: UniProt: R4NH29 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M carboxylic acids, 0.1M buffer system 1 pH 6.5, 30% P550MME_P20K, VAPOR DIFFUSION, SITTING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 65468 / % possible obs: 96.2 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 127.4 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 90.7 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.209 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.871 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.5 Å
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Refine LS restraints |
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