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Yorodumi- PDB-3r9k: Crystal structure of pyrophosphatase from bacteroides thetaiotaom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r9k | ||||||
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Title | Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, glu47asp mutant complexed with sulfate, a closed cap conformation | ||||||
Components | Putative beta-phosphoglucomutase | ||||||
Keywords | HYDROLASE / HOSPHOGLUCOMUTASE / PYROPHOSPHATASE / MAGNESIUM BINDING SITE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / ENZYME FUNCTION INITIATIVE / EFI / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information sugar-phosphatase activity / beta-phosphoglucomutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: Biochemistry / Year: 2011 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r9k.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r9k.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/3r9k ftp://data.pdbj.org/pub/pdb/validation_reports/r9/3r9k | HTTPS FTP |
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-Related structure data
Related structure data | 3qu2SC 3qu4C 3qu5C 3qu7C 3qu9C 3qubC 3qucC 3quqC 3qutC 3qx7C 3qxgC 3qypC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26993.848 Da / Num. of mol.: 1 / Mutation: E47D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_2127 / References: UniProt: Q8A5V9 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M TRIS-HCL, PH 8.5, 30% PEG4000, 200MM LITHIUM SULFATE, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 30588 / % possible obs: 99.7 % / Observed criterion σ(I): -5 / Redundancy: 9.4 % / Biso Wilson estimate: 36.459 Å2 / Rsym value: 0.071 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3QU2 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.728 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / 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: 44.127 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Total num. of bins used: 20
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