+Open data
-Basic information
Entry | Database: PDB / ID: 3iqa | ||||||
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Title | Crystal Structure of BlaC covalently bound with Doripenem | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / penicillin binding protein / beta-lactam covalent adduct / Antibiotic resistance / Cell membrane / Hydrolase / Lipoprotein / Membrane / Palmitate / HYDROLASE-HYDROLASE INHIBITOR 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: 2.2 Å | ||||||
Authors | Tremblay, L.W. / Blanchard, J.S. | ||||||
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 | 3iqa.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iqa.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iqa_validation.pdf.gz | 733.8 KB | Display | wwPDB validaton report |
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Full document | 3iqa_full_validation.pdf.gz | 734 KB | Display | |
Data in XML | 3iqa_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3iqa_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqa ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqa | HTTPS FTP |
-Related structure data
Related structure data | 3m6bC 3m6hC 3dwzS S: Starting model for refinement C: citing same article (ref.) |
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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) / Strain: H37Rv / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DRW / ( | #4: Water | ChemComp-HOH / | Nonpolymer details | DORIPENEM BETA-LACTAM RING OPEN AND COVALENTLY BOUND TO AMBLER NUMBERED RESIDUE SER70 (MTBLAC SER84) ...DORIPENEM BETA-LACTAM RING OPEN AND COVALENTLY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES pH 7.5, 2 M NH4H2PO4, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Monochromator: Si(111) Channel Cut / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 13696 / Num. obs: 13696 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 13.38 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / Num. unique all: 13695 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DWZ Resolution: 2.2→35.58 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.77 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.192 / 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: 53.02 Å2 / Biso mean: 8.264 Å2 / Biso min: 2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→35.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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