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- PDB-5zgi: Crystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zgi | ||||||
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Title | Crystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule per asymmetric unit | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
![]() | HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change / ANTIBIOTIC | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, H. / Hao, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1. Authors: Zhang, H. / Ma, G. / Zhu, Y. / Zeng, L. / Ahmad, A. / Wang, C. / Pang, B. / Fang, H. / Zhao, L. / Hao, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zgeC ![]() 5zgfC ![]() 5zgpC ![]() 5zgqC ![]() 5zgrC ![]() 5zgtC ![]() 5zguC ![]() 5zgvC ![]() 5zgwC ![]() 5zgxC ![]() 5zgyC ![]() 5zgzC ![]() 5zh1C ![]() 3q6x S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 346 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-OH / | #4: Chemical | #5: Chemical | ChemComp-SIN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.07 % / Mosaicity: 0.189 ° / Mosaicity esd: 0.002 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M sodium succinate pH6.5, 40% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.98→50 Å / Num. obs: 109068 / % possible obs: 93.5 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.095 / Χ2: 1.004 / Net I/σ(I): 12.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q6X ![]() 3q6x Resolution: 0.98→41.75 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.406 / SU ML: 0.011 / SU R Cruickshank DPI: 0.0197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.43 Å2 / Biso mean: 9.824 Å2 / Biso min: 4.09 Å2
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Refinement step | Cycle: final / Resolution: 0.98→41.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.98→1.005 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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