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- PDB-3mdq: Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytoph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mdq | ||||||
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Title | Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution | ||||||
![]() | Exopolyphosphatase | ||||||
![]() | HYDROLASE / Exopolyphosphatase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 69.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 452.1 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35777.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q11YA9, UniProt: A0A6N4SMU8*PLUS, exopolyphosphatase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.4500M ammonium sulfate, 13.6000% Glycerol, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→29.786 Å / Num. obs: 56714 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.011 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4) CHLORIDE (CL) AND SULFATE (SO4) IONS FROM CRYSTALLIZATION CONDITION, AND GLYCEROL (GOL) MOLECULES FROM EITHER CRYSTALLIZATION OR CRYO CONDITION ARE MODELED.
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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 max: 56.47 Å2 / Biso mean: 17.122 Å2 / Biso min: 5.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.786 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.3504 Å / Origin y: 4.7463 Å / Origin z: 69.2282 Å
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