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Yorodumi- PDB-6twt: Crystal structure of N-terminally truncated NDM-1 metallo-beta-la... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6twt | ||||||
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Title | Crystal structure of N-terminally truncated NDM-1 metallo-beta-lactamase | ||||||
Components | Metallo beta lactamase NDM-1 | ||||||
Keywords | HYDROLASE / METALLO-BETA-LACTAMASE / NDM-1 / antibiotic resistance | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Imiolczyk, B. / Czyrko-Horczak, J. / Brzezinski, K. / Jaskolski, M. | ||||||
Funding support | Poland, 1items
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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 | 6twt.cif.gz | 221.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6twt.ent.gz | 174.4 KB | Display | PDB format |
PDBx/mmJSON format | 6twt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/6twt ftp://data.pdbj.org/pub/pdb/validation_reports/tw/6twt | HTTPS FTP |
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-Related structure data
Related structure data | 6ogoC 6ol8C 3zr9S 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.2797550 / Data set type: diffraction image data |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25688.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, ...Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, p2146_00143, pCRE380_21, PMK1_ndm00067, PMK1_ndm00076, PMK1_ndm00085, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3531848_05178, TR3_031, TR4_031 Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5, UniProt: C7C422*PLUS |
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-Non-polymers , 5 types, 588 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 1.97 Å3/Da / Density % sol: 37.72 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MgCl2, CaCl2, imidazole, MES, MPD, PEG 1000, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8266 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→53.58 Å / Num. obs: 253359 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / CC1/2: 1 / Rrim(I) all: 0.064 / Net I/σ(I): 19.33 |
Reflection shell | Resolution: 0.95→1.01 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 40251 / CC1/2: 0.605 / Rrim(I) all: 1.592 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZR9 Resolution: 0.95→53.58 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.447 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0141 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.015 / Details: HYDROGEN ATOMS WERE ADDED AT 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 max: 53.84 Å2 / Biso mean: 13.159 Å2 / Biso min: 5.32 Å2
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Refinement step | Cycle: final / Resolution: 0.95→53.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.951→0.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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