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- PDB-3qu7: Crystal structure of pyrophosphatase from bacteroides thetaiotaom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qu7 | ||||||
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Title | Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, asp13asn mutant complexed with calcium and phosphate | ||||||
![]() | 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 | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.1 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qu2SC ![]() 3qu4C ![]() 3qu5C ![]() 3qu9C ![]() 3qubC ![]() 3qucC ![]() 3quqC ![]() 3qutC ![]() 3qx7C ![]() 3qxgC ![]() 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 27006.891 Da / Num. of mol.: 2 / Mutation: D13N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_2127 / References: UniProt: Q8A5V9, inorganic diphosphatase #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 294 K / pH: 4.5 Details: 0.1M SODIUM ACETATE, PH 4.5, 30% PEG400, 200MM CALCIUM ACETATE, 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: Nov 10, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 45325 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 6.1 % / Rsym value: 0.053 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QU2 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.216 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / 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: 47.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1709 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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