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Yorodumi- PDB-2jg1: STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jg1 | ||||||
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Title | STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE with cofactor and substrate | ||||||
Components | TAGATOSE-6-PHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE / D-TAGATOSE-6-PHOSPHATE KINASE / PHOSPHORYL TRANSFER / CONFORMATIONAL CHANGES / KINASE / LACTOSE METABOLISM | ||||||
Function / homology | Function and homology information tagatose-6-phosphate kinase / phosphofructokinase activity / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Miallau, L. / Hunter, W.N. / McSweeney, S.M. / Leonard, G.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structures of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase Implicate Domain Motions in Specificity and Mechanism. Authors: Miallau, L. / Hunter, W.N. / Mcsweeney, S.M. / Leonard, G.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jg1.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jg1.ent.gz | 224.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jg1_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2jg1_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2jg1_validation.xml.gz | 56.7 KB | Display | |
Data in CIF | 2jg1_validation.cif.gz | 81.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jg1 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jg1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 36325.184 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: NCTC 8325 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A0B9, tagatose-6-phosphate kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ANP / #4: Sugar | ChemComp-TA6 / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 124 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 125 TO MSE ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 6.5 Details: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 0.1 M SODIUM CACODYLATE PH 6.5, 10% PEG 8000, 15% PEG 550, 10 MM ATP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.8 Å / Num. obs: 96948 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→24.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.131 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.85 Å
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Refine LS restraints |
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