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Yorodumi- PDB-4ock: N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ock | |||||||||
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Title | N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc and AMPPNP | |||||||||
Components | N-acetylhexosamine 1-phosphate kinase | |||||||||
Keywords | TRANSFERASE / kinase / sugar 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 / MOLECULAR REPLACEMENT / Resolution: 1.72 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ock.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ock.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ock.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/4ock ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4ock | HTTPS FTP |
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-Related structure data
Related structure data | 4ocjSC 4ocoC 4ocpC 4ocqC 4ocuC 4ocvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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#2: Sugar | ChemComp-NDG / |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2012 |
Radiation | Monochromator: LN2-cooled, fixed-exit double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→30 Å / Num. all: 43636 / Num. obs: 43636 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 26.69 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.78 / Rsym value: 0.492 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4OCJ Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.736 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.101 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.706 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.764 Å / Total num. of bins used: 20
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