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Yorodumi- PDB-4xh4: Crystal structure of Salmonella typhimurium propionate kinase A88... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xh4 | ||||||
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Title | Crystal structure of Salmonella typhimurium propionate kinase A88V mutant, in complex with AMPPNP and propionate | ||||||
Components | Propionate kinase | ||||||
Keywords | TRANSFERASE / KINASE / TDCD / AMPPNP / PROPIONATE | ||||||
Function / homology | Function and homology information propionate kinase / propionate kinase activity / L-threonine catabolic process to propionate / acetate kinase activity / acetate metabolic process / phosphorylation / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Murthy, A.M.V. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism Authors: Murthy, A.M.V. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xh4.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xh4.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xh4 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xh4 | HTTPS FTP |
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-Related structure data
Related structure data | 4xh1C 4xh5C 2e1yS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45405.645 Da / Num. of mol.: 1 / Fragment: UNP residues 1-402 / Mutation: A88V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: tdcD, oxd-2, STM3242 / Plasmid: PRSET C PRSET C PRSETPRSET PRSET C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06961, propionate kinase |
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-Non-polymers , 5 types, 139 molecules
#2: Chemical | ChemComp-ANP / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-PPI / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, 30% pentaerythritol ethoxylate, 0.05 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2014 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.03 Å / Num. obs: 42396 / % possible obs: 96.9 % / Redundancy: 4.7 % / Rsym value: 0.047 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E1Y Resolution: 1.8→32.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.93 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.676 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32.03 Å
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Refine LS restraints |
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