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- PDB-7wi1: The mutant variant of PNGM-1, H93 was substituuted for alanine to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wi1 | ||||||
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Title | The mutant variant of PNGM-1, H93 was substituuted for alanine to study metal coordination | ||||||
![]() | Metallo-beta-lactamase PNGM-1 | ||||||
![]() | HYDROLASE / RNase Z / MBLs / Zinc binding motif / ANTIBIOTIC | ||||||
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. | ||||||
Funding support | 1items
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![]() | ![]() 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 | ![]() | 588.8 KB | Display | ![]() |
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PDB format | ![]() | 486.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.4 MB | Display | ![]() |
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Full document | ![]() | 5.4 MB | Display | |
Data in XML | ![]() | 110.8 KB | Display | |
Data in CIF | ![]() | 155.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7byqC ![]() 7bz1C ![]() 7bz3C ![]() 7bz4C ![]() 7bziC ![]() 6j4nS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41634.453 Da / Num. of mol.: 8 / Mutation: H93A 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 287 K / Method: evaporation / pH: 7.1 Details: 50 mM HEPES pH 7.1, 10% PEG 4000, 150 mM Magnesium acetate, 200 mM Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: steady flow of liquid nitrogen / 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: 1.00003 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→50 Å / Num. obs: 388155 / % possible obs: 99.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Χ2: 1.477 / Net I/σ(I): 8.6 / Num. measured all: 2483252 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6j4n Resolution: 1.61→41.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.688 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / 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: 95.02 Å2 / Biso mean: 13.337 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 1.61→41.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.611→1.653 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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