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Yorodumi- PDB-3qfn: Crystal structure of Streptococcal asymmetric Ap4A hydrolase and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qfn | ||||||
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Title | Crystal structure of Streptococcal asymmetric Ap4A hydrolase and phosphodiesterase Spr1479/SapH in complex with inorganic phosphate | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | HYDROLASE / sandwich fold / Fe3+ / Mn2+ / PO4 | ||||||
Function / homology | Function and homology information phosphatase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Jiang, Y.L. / Zhang, J.W. / Yu, W.L. / Cheng, W. / Zhang, C.C. / Zhou, C.Z. / Chen, Y. | ||||||
Citation | Journal: To be Published Title: Structural and enzymatic characterization of a Streptococcal ATP/diadenosine polyphosphate and phosphodiester hydrolase Spr1479/SapH Authors: Jiang, Y.L. / Zhang, J.W. / Yu, W.L. / Cheng, W. / Zhang, C.C. / Frolet, C. / Di-guilmi, A.-M. / Vernet, T. / Zhou, C.Z. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qfn.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qfn.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/3qfn ftp://data.pdbj.org/pub/pdb/validation_reports/qf/3qfn | HTTPS FTP |
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-Related structure data
Related structure data | 3qfmSC 3qfoC S: Starting model for refinement 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: 31422.646 Da / Num. of mol.: 2 / Fragment: UNP residues 1-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr1479 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8DNX4 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% iso-propanol, 0.1M HEPES, pH 7.5, 0.2M NH4Ac, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 28781 / % possible obs: 95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2920 / Rsym value: 0.517 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QFM Resolution: 2.31→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.595 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / 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: 35.391 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.307→2.367 Å / Total num. of bins used: 20
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