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- PDB-3qxg: Crystal structure of pyrophosphatase from bacteroides thetaiotaom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qxg | ||||||
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Title | Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation | ||||||
![]() | INORGANIC PYROPHOSPHATASE | ||||||
![]() | HYDROLASE / PYROPHOSPHATASE / MAGNESIUM BINDING SITE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / ENZYME FUNCTION INITIATIVE / EFI / PSI-2 / Protein Structure Initiative / NYSGXRC | ||||||
Function / homology | ![]() 2-deoxyglucose-6-phosphatase activity / glycerol-3-phosphatase activity / sugar-phosphatase activity / beta-phosphoglucomutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Huang, H. / Toro, R. / Gerlt, J.A. / Burley, S.K. / Dunaway-Mariano, D. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) / Enzyme Function Initiative (EFI) | ||||||
![]() | ![]() Title: Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 Is an Inorganic Pyrophosphatase. Authors: Huang, H. / Patskovsky, Y. / Toro, R. / Farelli, J.D. / Pandya, C. / Almo, S.C. / Allen, K.N. / Dunaway-Mariano, D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222 KB | Display | ![]() |
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PDB format | ![]() | 176.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.6 KB | Display | ![]() |
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Full document | ![]() | 470.7 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qu2SC ![]() 3qu4C ![]() 3qu5C ![]() 3qu7C ![]() 3qu9C ![]() 3qubC ![]() 3qucC ![]() 3quqC ![]() 3qutC ![]() 3qx7C ![]() 3qypC ![]() 3r9kC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27007.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_2127 / References: UniProt: Q8A5V9, inorganic diphosphatase |
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-Non-polymers , 6 types, 540 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-TLA / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M SODIUM ACETATE, PH 4.5, 0.2M CALCIUM ACETATE, 30% PEG400, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→50 Å / Num. obs: 147352 / % possible obs: 99 % / Observed criterion σ(I): -5 / Redundancy: 3 % / Biso Wilson estimate: 13.32 Å2 / Rsym value: 0.056 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.9 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3QU2 Resolution: 1.24→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.668 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R Free: 0.039 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.243→1.275 Å / Total num. of bins used: 20
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