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Yorodumi- PDB-3qyp: Crystal structure of pyrophosphatase from bacteroides thetaiotaom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qyp | ||||||
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Title | Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, glu47asn mutant complexed with calcium and phosphate | ||||||
Components | INORGANIC PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / PYROPHOSPHATASE / MAGNESIUM BINDING SITE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGX ENZYME FUNCTION INITIATIVE / EFI / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NYSGXRC | ||||||
Function / homology | Function and homology information beta-phosphoglucomutase activity / sugar-phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.6 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 | 3qyp.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qyp.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qyp_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 3qyp_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 3qyp_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3qyp_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/3qyp ftp://data.pdbj.org/pub/pdb/validation_reports/qy/3qyp | HTTPS FTP |
-Related structure data
Related structure data | 3qu2SC 3qu4C 3qu5C 3qu7C 3qu9C 3qubC 3qucC 3quqC 3qutC 3qx7C 3qxgC 3r9kC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26992.863 Da / Num. of mol.: 2 / Mutation: E47N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_2127 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8A5V9, inorganic diphosphatase |
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-Non-polymers , 6 types, 475 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M MES, PH 6.0, 20% PEG8000, 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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 |
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: 1.6→50 Å / Num. obs: 61148 / % possible obs: 95.3 % / Observed criterion σ(I): -5 / Redundancy: 3.9 % / Biso Wilson estimate: 23.108 Å2 / Rsym value: 0.065 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / % possible all: 69 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 3QU2 Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.093 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / 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: 29.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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