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Yorodumi- PDB-3m6h: Crystal Structure of Post-isomerized Ertapenem Covalent Adduct wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m6h | ||||||
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Title | Crystal Structure of Post-isomerized Ertapenem Covalent Adduct with TB B-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/Antibiotic / alpha-beta structure / Antibiotic resistance / Cell membrane / Hydrolase / Lipoprotein / Membrane / Palmitate / Hydrolase-Antibiotic complex | ||||||
Function / homology | Function and homology information : / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å | ||||||
Authors | Tremblay, L.W. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Biochemical and structural characterization of Mycobacterium tuberculosis beta-lactamase with the carbapenems ertapenem and doripenem. Authors: Tremblay, L.W. / Fan, F. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m6h.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m6h.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m6h_validation.pdf.gz | 740 KB | Display | wwPDB validaton report |
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Full document | 3m6h_full_validation.pdf.gz | 740 KB | Display | |
Data in XML | 3m6h_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3m6h_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/3m6h ftp://data.pdbj.org/pub/pdb/validation_reports/m6/3m6h | HTTPS FTP |
-Related structure data
Related structure data | 3iqaC 3m6bC 3dwzS C: citing same article (ref.) 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
#1: Protein | Mass: 28272.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, Rv2068c, MT2128, MTCY49.07c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-2RG / ( | #4: 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: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 4.1 Details: 0.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 8, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.994→50 Å / Num. all: 18010 / Num. obs: 17920 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.191 / Χ2: 1.932 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.994→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 4 / Num. unique all: 1762 / Χ2: 1.788 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DWZ Resolution: 1.994→30.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.356 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.162 / 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 max: 31.21 Å2 / Biso mean: 6.842 Å2 / Biso min: 2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.994→30.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.994→2.046 Å / Total num. of bins used: 20
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