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- PDB-6jdo: Crystal structure of N-acetyl mannosmaine kinase with AMP-PNP fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jdo | |||||||||
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Title | Crystal structure of N-acetyl mannosmaine kinase with AMP-PNP 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 | ![]() | 131.9 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jdaSC ![]() 6jdbC ![]() 6jdcC ![]() 6jdhC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 30874.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A2K0XYW4, UniProt: Q9CKB3*PLUS, N-acylmannosamine kinase #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: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M Tascimate 5.0, 20% v/v isopropanol, 20% w/v PEG 4000, 100% v/v ethylene glycol |
-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 1, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→45.69 Å / Num. obs: 51733 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 15 / Num. measured all: 514396 / Scaling rejects: 22 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JDA Resolution: 2.002→38.77 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.76 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: 87.23 Å2 / Biso mean: 43.643 Å2 / Biso min: 23.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.002→38.77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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