+Open data
-Basic information
Entry | Database: PDB / ID: 4ocj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc | |||||||||
Components | N-acetylhexosamine 1-phosphate kinase | |||||||||
Keywords | TRANSFERASE / kinase / ATP binding | |||||||||
Function / homology | Function and homology information N-acetylhexosamine 1-kinase / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / homoserine kinase activity / phosphotransferase activity, alcohol group as acceptor / threonine biosynthetic process / transferase activity / carbohydrate metabolic process / hydrolase activity / phosphorylation / ATP binding Similarity search - Function | |||||||||
Biological species | Bifidobacterium longum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.571 Å | |||||||||
Authors | Li, T.L. / Wang, K.C. / Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes. Authors: Wang, K.C. / Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / Li, T.L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ocj.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ocj.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ocj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/4ocj ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4ocj | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ockC 4ocoC 4ocpC 4ocqC 4ocuC 4ocvC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42660.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: mdsC, BN57_1851 / Production host: Escherichia coli (E. coli) References: UniProt: T2I3Q3, UniProt: E8MF12*PLUS, N-acetylhexosamine 1-kinase |
---|---|
#2: Sugar | ChemComp-NDG / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97874, 0.97893, 0.96353 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2013 | ||||||||||||
Radiation | Monochromator: LN2-cooled, fixed-exit double crystal Si(111) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.571→30 Å / Num. all: 56696 / Num. obs: 56696 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 130.12 | ||||||||||||
Reflection shell | Resolution: 1.571→1.66 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6 / Rsym value: 0.447 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.571→25.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.217 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.678 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.571→25.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.571→1.612 Å / Total num. of bins used: 20
|