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Yorodumi- PDB-5a60: Crystal structure of full-length E. coli ygiF in complex with tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a60 | ||||||
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Title | Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two magnesium ions | ||||||
Components | INORGANIC TRIPHOSPHATASE | ||||||
Keywords | HYDROLASE / INORGANIC POLYPHOSPHATE / TRIPOLYPHOSPHATE / TRIPHOSPHATE TUNNEL METALLOENZYMES | ||||||
Function / homology | Function and homology information triphosphatase / inorganic triphosphate phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å | ||||||
Authors | Martinez, J. / Truffault, V. / Hothorn, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. Authors: Martinez, J. / Truffault, V. / Hothorn, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a60.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a60.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/5a60 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a60 | HTTPS FTP |
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-Related structure data
Related structure data | 5a5yC 5a61C 5a64C 5a65C 5a66C 5a67C 5a68C 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: 48638.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL References: UniProt: V8FJJ2, UniProt: P30871*PLUS, triphosphatase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-3PO / | #4: Chemical | #5: 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: 3.01 Å3/Da / Density % sol: 59.18 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3,350, 0.2 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 |
Detector | Type: DECTRIS HYBRID PHOTON / Date: Mar 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→48.88 Å / Num. obs: 50673 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.91 |
Reflection shell | Resolution: 1.82→1.93 Å / Redundancy: 9.06 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.18 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.82→48.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 6.625 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 55.658 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→48.88 Å
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Refine LS restraints |
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