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- PDB-3fdz: Crystal structure of phosphoglyceromutase from burkholderia pseud... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fdz | ||||||
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Title | Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b with bound 2,3-diphosphoglyceric acid and 3-phosphoglyceric acid | ||||||
![]() | (2,3-bisphosphoglycerate-dependent phosphoglycerate ...) x 2 | ||||||
![]() | ISOMERASE / SSGCID / Phosphoglyceromutase / Burkholderia pseudomallei / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. Authors: Davies, D.R. / Staker, B.L. / Abendroth, J.A. / Edwards, T.E. / Hartley, R. / Leonard, J. / Kim, H. / Rychel, A.L. / Hewitt, S.N. / Myler, P.J. / Stewart, L.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.2 KB | Display | ![]() |
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Full document | ![]() | 798.3 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eznC ![]() 3gp3C ![]() 3gp5C ![]() 3gw8C ![]() 3lntC 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | The asymmetric unit contains two biological units |
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Components
-2,3-bisphosphoglycerate-dependent phosphoglycerate ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28958.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1719B / Gene: BURPS1710b_0662, gpmA / Plasmid: AVA0421 / Production host: ![]() ![]() |
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#2: Protein | Mass: 29037.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1719B / Gene: BURPS1710b_0662, gpmA / Plasmid: AVA0421 / Production host: ![]() ![]() |
-Non-polymers , 4 types, 227 molecules ![](data/chem/img/DG2.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/3PG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/3PG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-DG2 / ( | ||||
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#4: Chemical | #5: Chemical | ChemComp-3PG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 289 K / pH: 6 Details: 30% PEG 600, 5% PEG 1000, 10% GLYCEROL, 100 MM MES PH 6.0, CRYSTALS SOAKED OVERNIGHT WITH 20 MM 3-PHOSPHOGLYCERIC ACID, VAPOR DIFFUSION, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SATURN / Detector: CCD / Date: Sep 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 20934 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.18 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.43 |
Reflection shell | Resolution: 2.25→2.31 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.6 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 23.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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