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Yorodumi- PDB-3shd: Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3shd | ||||||
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Title | Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1 | ||||||
Components | Phosphatase nudJ | ||||||
Keywords | HYDROLASE / Nudix fold / Nudix motif / (d)NDP/(d)NTP binding / dephosphorylation | ||||||
Function / homology | Function and homology information thiamine diphosphate phosphatase activity / nucleoside diphosphate phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribonucleoside triphosphate phosphatase activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hong, M.K. / Kim, J.K. / Kang, L.W. | ||||||
Citation | Journal: To be Published Title: Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli Authors: Hong, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3shd.cif.gz | 373.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3shd.ent.gz | 307.1 KB | Display | PDB format |
PDBx/mmJSON format | 3shd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3shd_validation.pdf.gz | 558.5 KB | Display | wwPDB validaton report |
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Full document | 3shd_full_validation.pdf.gz | 622.5 KB | Display | |
Data in XML | 3shd_validation.xml.gz | 73.2 KB | Display | |
Data in CIF | 3shd_validation.cif.gz | 97.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/3shd ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3shd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
-Components
#1: Protein | Mass: 17450.854 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O1:K1 / APEC / Gene: nudJ, Ecok1_10240, APECO1_216 / Production host: Escherichia coli (E. coli) References: UniProt: A1AA28, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 3.65 Å3/Da / Density % sol: 66.26 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.4M ammonium sulfate, 0.1M MES buffer pH 6.0, 100mM MnCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 182291 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→50 Å / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.797 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.301 / 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: 38.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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