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- PDB-5zh1: Crystal structure of NDM-1 at pH7.5 (Imidazole) with 2 molecules ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zh1 | ||||||
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Title | Crystal structure of NDM-1 at pH7.5 (Imidazole) with 2 molecules per asymmetric unit | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
![]() | HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change | ||||||
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 | ![]() | 219.5 KB | Display | ![]() |
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PDB format | ![]() | 174.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.2 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zgeC ![]() 5zgfC ![]() 5zgiC ![]() 5zgpC ![]() 5zgqC ![]() 5zgrC ![]() 5zgtC ![]() 5zguC ![]() 5zgvC ![]() 5zgwC ![]() 5zgxC ![]() 5zgyC ![]() 5zgzC ![]() 3q6x C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 30 - 268 / Label seq-ID: 2 - 240
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Components
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.42 % / Mosaicity: 0.182 ° / Mosaicity esd: 0.003 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M imidazole pH7.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.93924 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→50 Å / Num. obs: 168917 / % possible obs: 94.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.065 / Χ2: 0.97 / Net I/σ(I): 10.1 / Num. measured all: 1268191 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q6X ![]() 3q6x Resolution: 1.05→32.75 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.978 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.031 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: 101.54 Å2 / Biso mean: 23.372 Å2 / Biso min: 15.5 Å2
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Refinement step | Cycle: final / Resolution: 1.05→32.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13675 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.054→1.081 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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