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Yorodumi- PDB-4pnh: Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pnh | |||||||||
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Title | Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase from Burkholderia Thailandensis | |||||||||
Components | D,D-heptose 1,7-bisphosphate phosphatase | |||||||||
Keywords | HYDROLASE / GMHB / ALPHA/BETA / PHOSPHATASE / D / D-HEPTOSE 1 / 7-BISPHOSPHATE | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / carbohydrate metabolic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Burkholderia thailandensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | |||||||||
Authors | Kim, M.S. / Shin, D.H. | |||||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase from Burkholderia Thailandensis Authors: Kim, M.S. / Shin, D.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pnh.cif.gz | 345.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pnh.ent.gz | 291.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/4pnh ftp://data.pdbj.org/pub/pdb/validation_reports/pn/4pnh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21368.496 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0583 / Production host: Escherichia coli (E. coli) References: UniProt: Q2T109, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.3M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2009 |
Radiation | Monochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→48.86 Å / Num. obs: 70758 / % possible obs: 87.9 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.66→2.71 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.1 / % possible all: 86.1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1420) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→35.01 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.84 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→35.01 Å
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Refine LS restraints |
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LS refinement shell |
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