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Yorodumi- PDB-2enx: Structure of the family II inorganic pyrophosphatase from Strepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2enx | ||||||
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Title | Structure of the family II inorganic pyrophosphatase from Streptococcus agalactiae at 2.8 resolution | ||||||
Components | Manganese-dependent inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / Streptococcus agalactiae / family II / inorganic / pyrophosphatase / signalling / phosphorylation | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Rantanen, M.K. / Lehtio, L. / Rajagopal, L. / Rubens, C.E. / Goldman, A. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007 Title: Structure of the Streptococcus agalactiae family II inorganic pyrophosphatase at 2.80 A resolution Authors: Rantanen, M.K. / Lehtio, L. / Rajagopal, L. / Rubens, C.E. / Goldman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2enx.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2enx.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 2enx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/2enx ftp://data.pdbj.org/pub/pdb/validation_reports/en/2enx | HTTPS FTP |
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-Related structure data
Related structure data | 1i74S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 2 - 311 / Label seq-ID: 1 - 310
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Details | The second part of the biological assembly is generated by the two fold axis: -x+1, -y, z+3/2. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33492.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: A909 / Gene: ppaC / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3K0B5, inorganic diphosphatase |
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-Non-polymers , 5 types, 165 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.2 Details: 0.4M ammonium phosphate monobasic, pH 4.2, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.5 Å / Num. all: 20708 / Num. obs: 20700 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.2 / Num. unique all: 1903 / Rsym value: 0.3 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I74 Resolution: 2.8→19.5 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.807 / SU B: 14.887 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.548 / ESU R Free: 0.38 / 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: 18.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 2357 / Type: medium positional / Rms dev position: 0.32 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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