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Open data
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Basic information
Entry | Database: PDB / ID: 1ggo | ||||||
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Title | T453A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE | ||||||
![]() | PROTEIN (PYRUVATE, PHOSPHATE DIKINASE) | ||||||
![]() | TRANSFERASE / PHOSPHOTRANSFERASE / KINASE | ||||||
Function / homology | ![]() pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Li, Z. / Herzberg, O. | ||||||
![]() | ![]() Title: Identification of domain-domain docking sites within Clostridium symbiosum pyruvate phosphate dikinase by amino acid replacement. Authors: Wei, M. / Li, Z. / Ye, D. / Herzberg, O. / Dunaway-Mariano, D. #1: ![]() Title: Swiveling-Domain Mechanism for Enzymatic Phosphotransfer between Remote Reaction Sites Authors: Herzberg, O. / Chen, C.C. / Kapadia, G. / McGuire, M. / Carroll, L.J. / Noh, S.J. / Dunaway-Mariano, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.4 KB | Display | ![]() |
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PDB format | ![]() | 143.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 386.5 KB | Display | ![]() |
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Full document | ![]() | 446.9 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 96610.125 Da / Num. of mol.: 1 / Mutation: T453A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 15, 1999 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 27567 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.236 / % possible all: 68 |
Reflection | *PLUS Num. measured all: 43302 |
Reflection shell | *PLUS % possible obs: 68 % |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.6→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Bsol: 64 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.7 |