+Open data
-Basic information
Entry | Database: PDB / ID: 7ct2 | |||||||||
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Title | New Delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q | |||||||||
Components | Metallo beta lactamase NDM-1 | |||||||||
Keywords | HYDROLASE / Apo | |||||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / antibiotic catabolic process / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / beta-lactamase / metal ion binding / Metallo-beta-lactamase type 2 Function and homology information | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Kong, W.P. / Chen, Y.W. / Wong, K.Y. | |||||||||
Funding support | China, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2022 Title: The crystal structure of the H116Q mutant of NDM-1: An enzyme devoid of zinc ions. Authors: Kong, W.P. / Chen, Y.W. / Wong, K.Y. #1: Journal: Biochim Biophys Acta Proteins Proteom / Year: 2022 Title: NDM-1 Zn1-binding residue His116 plays critical roles in antibiotic hydrolysis. Authors: Fung, Y.H. / Kong, W.P. / Leung, A.S.L. / Du, R. / So, P.K. / Wong, W.L. / Leung, Y.C. / Chen, Y.W. / Wong, K.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ct2.cif.gz | 201.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ct2.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ct2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ct2_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 7ct2_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 7ct2_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 7ct2_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/7ct2 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/7ct2 | HTTPS FTP |
-Related structure data
Related structure data | 5zgyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26533.773 Da / Num. of mol.: 4 / Mutation: H116Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: NDM-1, bla NDM-1, blaNDM-1, blaNDM1, D647_p47098, DBX64_28130, DDJ63_29735, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3499901_05193, TR3_031, TR4_031 Plasmid: pET28a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: E9NWK5 #2: Water | ChemComp-HOH / | 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: 2.24 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% PEG 3350, 100 mM Sodium succinate, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.3 Å / Num. obs: 56672 / % possible obs: 92.7 % / Redundancy: 2 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.09 / Rrim(I) all: 0.128 / Rsym value: 0.09 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3 / Num. unique obs: 7888 / Rpim(I) all: 0.242 / Rrim(I) all: 0.342 / Rsym value: 0.242 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZGY Resolution: 1.95→30.538 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.311 / WRfactor Rwork: 0.24 / SU B: 6.462 / SU ML: 0.18 / Average fsc free: 0.8295 / Average fsc work: 0.8605 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.216 Details: Hydrogens have been used if present in the input file
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.251 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30.538 Å
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Refine LS restraints |
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LS refinement shell |
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