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Yorodumi- PDB-6c89: NDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c89 | ||||||
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Title | NDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements for the Hydrolysis of Penicillin versus Carbapenem Antibiotics | ||||||
Components | Beta-lactamase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / NDM-1 / beta-lactamase / deep sequencing / antibiotic resistance / beta-lactams | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / antibiotic catabolic process / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase / hydrolase activity / metal ion binding / Metallo-beta-lactamase type 2 Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75006148726 Å | ||||||
Authors | Palzkill, T. / Sun, Z. / Sankaran, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Differential active site requirements for NDM-1 beta-lactamase hydrolysis of carbapenem versus penicillin and cephalosporin antibiotics. Authors: Sun, Z. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c89.cif.gz | 241.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c89.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 6c89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c89_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 6c89_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | 6c89_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 6c89_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/6c89 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/6c89 | HTTPS FTP |
-Related structure data
Related structure data | 3q6x S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24475.492 Da / Num. of mol.: 4 / Mutation: K224R/G232A/N233Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaNDM-1, bla NDM-1, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5KIY2 |
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-Non-polymers , 6 types, 690 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 2.15 Å3/Da / Density % sol: 42.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M LiCl, 0.1 M HEPES, pH7.0, 20% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.668 Å / Num. obs: 75377 / % possible obs: 91.07 % / Redundancy: 2.3 % / Biso Wilson estimate: 16.0102224723 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.75→1.813 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.325 / Num. unique obs: 4529 / % possible all: 54.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q6X 3q6x Resolution: 1.75006148726→37.2364552136 Å / SU ML: 0.172754826987 / Cross valid method: FREE R-VALUE / σ(F): 1.96361990839 / Phase error: 20.1253550062 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: 19.4899005082 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75006148726→37.2364552136 Å
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Refine LS restraints |
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LS refinement shell |
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