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- PDB-7byq: The mutant variant of PNGM-1. H279A was substituted for alanine t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7byq | ||||||
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Title | The mutant variant of PNGM-1. H279A was substituted for alanine to study metal coordination. | ||||||
![]() | Metallo-beta-lactamase PNGM-1 | ||||||
![]() | ANTIBIOTIC / RNase Z / MBLs / Zinc binding motif | ||||||
Function / homology | 3'-tRNA processing endoribonuclease activity / Beta-lactamase superfamily domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / beta-lactamase / metal ion binding / Metallo-beta-lactamase PNGM-1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | PNGM-1 residue H91 was substituted to Alanine | ||||||
![]() | Park, Y.S. / Kang, L.W. / Lee, J.H. | ||||||
![]() | ![]() Title: Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants. Authors: Park, Y.S. / Kim, T.Y. / Park, H. / Lee, J.H. / Nguyen, D.Q. / Hong, M.K. / Lee, S.H. / Kang, L.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.5 KB | Display | ![]() |
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PDB format | ![]() | 241.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 87.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bz1C ![]() 7bz3C ![]() 7bz4C ![]() 7bziC ![]() 7wi1C ![]() 6j4nS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41634.457 Da / Num. of mol.: 4 / Mutation: H279A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.45 % / Mosaicity: 0.804 ° |
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Crystal grow | Temperature: 287 K / Method: evaporation / pH: 5.4 Details: 0.1 M Sodium acetate, 1.5 M Sodium formate, 0.08 M CaCl2 and 10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: steady flow of liquid nitrogen was used to maintain 100 K. Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→50 Å / Num. obs: 211626 / % possible obs: 96.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.055 / Rrim(I) all: 0.134 / Χ2: 1.16 / Net I/σ(I): 5.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6j4n Resolution: 1.96→49.04 Å / Cor.coef. Fo:Fc: 0.523 / Cor.coef. Fo:Fc free: 0.434 / SU B: 18.309 / SU ML: 0.546 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 120.5 Å2 / Biso mean: 20.693 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 1.96→49.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→1.989 Å / Rfactor Rfree error: 0
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