+Open data
-Basic information
Entry | Database: PDB / ID: 1kt9 | ||||||
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Title | Crystal Structure of C. elegans Ap4A Hydrolase | ||||||
Components | Diadenosine Tetraphosphate Hydrolase | ||||||
Keywords | HYDROLASE / Nudix | ||||||
Function / homology | Function and homology information 5-phosphoribosyl 1-pyrophosphate pyrophosphatase activity / diadenosine tetraphosphate catabolic process / Detoxification of Reactive Oxygen Species / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / AMP biosynthetic process / ADP biosynthetic process / ribose phosphate metabolic process / ATP biosynthetic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / apoptotic process / ATP binding Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å | ||||||
Authors | Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, H.M. / Baker, P.J. / McLennan, A.G. / Rafferty, J.B. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms Authors: Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, H.M. / Baker, P.J. / McLennan, A.G. / Rafferty, J.B. #1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2001 Title: Cloning, characterisation and crystallisation of a diadenosine 5',5"'-P(1),P(4)-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans. Authors: Abdelghany, H.M. / Gasmi, L. / Cartwright, J.L. / Bailey, S. / Rafferty, J.B. / McLennan, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kt9.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kt9.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kt9 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kt9 | HTTPS FTP |
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-Related 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: 15913.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Y37H9A.6 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9U2M7, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) |
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#2: 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: 2.2 Å3/Da / Density % sol: 43.97 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→18 Å / Num. all: 53439 / Num. obs: 9864 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.98→2.05 Å / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 18 Å / % possible obs: 97.9 % / Num. measured all: 53439 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 9.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.165 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.15 / Stereochemistry target values: Engh & Huber / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.727 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 18.7636 Å / Origin y: 14.3648 Å / Origin z: 8.2546 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 18 Å / Rfactor obs: 0.201 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.201 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.203 |