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- PDB-6jdh: Crystal structure of N-acetyl mannosmaine kinase from Pasteurella... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jdh | |||||||||
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Title | Crystal structure of N-acetyl mannosmaine kinase from Pasteurella multocida | |||||||||
![]() | N-acetylmannosamine kinase | |||||||||
![]() | SUGAR BINDING PROTEIN / Kinase / ManNAc binding protein / two domain protein | |||||||||
Function / homology | ![]() N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylmannosamine metabolic process / N-acetylneuraminate catabolic process / zinc ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Thanuja, G. / Ramaswamy, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Function of N‐Acetylmannosamine Kinases from Pathogenic Bacteria. Authors: Thanuja, G. / Ramaswamy, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.1 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jdaSC ![]() 6jdbC ![]() 6jdcC ![]() 6jdoC 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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Unit cell |
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Components
#1: Protein | Mass: 31353.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ROK kinase / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tascimate 5.0, 20% v/v Isopropanol, 20% w/v PEG 4000 with an additive containing 2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→45.58 Å / Num. obs: 59936 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.027 / Rrim(I) all: 0.085 / Net I/σ(I): 17.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JDA Resolution: 1.9→38.565 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.61 Å2 / Biso mean: 38.7923 Å2 / Biso min: 16.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→38.565 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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