+Open data
-Basic information
Entry | Database: PDB / ID: 6ogo | |||||||||
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Title | Crystal structure of NDM-9 metallo-beta-lactamase | |||||||||
Components | SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9 | |||||||||
Keywords | HYDROLASE / metallo-beta-lactamase / NDM | |||||||||
Function / homology | Function and homology information Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | |||||||||
Authors | Raczynska, J.E. / Imiolczyk, B. / Jaskolski, M. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates. Authors: Raczynska, J.E. / Imiolczyk, B. / Komorowska, M. / Sliwiak, J. / Czyrko-Horczak, J. / Brzezinski, K. / Jaskolski, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ogo.cif.gz | 311.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ogo.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ogo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/6ogo ftp://data.pdbj.org/pub/pdb/validation_reports/og/6ogo | HTTPS FTP |
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-Related structure data
Related structure data | 6ol8C 6twtC 3q6x S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18150/repod.8876113 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 25688.941 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: BK248_28090, BK292_25365, BK373_25580, BK383_27845, CA593_27010 Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M2CSI6 |
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-Non-polymers , 8 types, 808 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | #8: Chemical | #9: 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: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2M NaCl, 0.1M Phosphate/citrate pH 4.2, 20% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.72931 Å | |||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2017 | |||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.72931 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.43→61.46 Å / Num. obs: 120161 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.088 / Net I/σ(I): 16.5 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.43→1.52 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 19202 / CC1/2: 0.71 / Rrim(I) all: 0.782 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3q6x 3q6x Resolution: 1.43→61.46 Å / Cor.coef. Fo:Fc: 0.992 / Cor.coef. Fo:Fc free: 0.983 / SU B: 1.009 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.007 / ESU R Free: 0.008 / Details: HYDROGENS WERE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.072 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→61.46 Å
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Refine LS restraints |
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