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- PDB-6jdc: Crystal structure of N-acetyl mannosmaine kinase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jdc | |||||||||
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Title | Crystal structure of N-acetyl mannosmaine kinase in complex with ManNAc from Haemophilus influenzae | |||||||||
![]() | 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 | ![]() | 67 KB | Display | ![]() |
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PDB format | ![]() | 47.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jdaC ![]() 6jdbSC ![]() 6jdhC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30920.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 86-028NP / Gene: nanK / Production host: ![]() ![]() |
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#2: Sugar | ChemComp-BM3 / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M sodium malonate 7.0, 20% w/v PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.865 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.22→46.01 Å / Num. obs: 19197 / % possible obs: 98.1 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.042 / Rrim(I) all: 0.084 / Net I/σ(I): 11.3 / Num. measured all: 69837 / Scaling rejects: 1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JDB Resolution: 2.271→46.008 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 27.59 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.09 Å2 / Biso mean: 44.5861 Å2 / Biso min: 23.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.271→46.008 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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