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- PDB-1gyx: The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Hom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gyx | ||||||
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Title | The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity | ||||||
![]() | HYPOTHETICAL PROTEIN YDCE | ||||||
![]() | ISOMERASE / TAUTOMERASE / HYPOTHETICAL PROTEIN / COMPLETE PROTEO | ||||||
Function / homology | ![]() intramolecular oxidoreductase activity, interconverting keto- and enol-groups / Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / : / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Almrud, J. / Kern, A. / Wang, S. / Czerwinski, R. / Johnson, W. / Murzin, A. / Hackert, M. / Whitman, C. | ||||||
![]() | ![]() Title: The Crystal Structure of Ydce, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia Coli, Confirms the Structural Basis for Oligomer Diversity Authors: Almrud, J. / Kern, A. / Wang, S. / Czerwinski, R. / Johnson, W. / Murzin, A. / Hackert, M. / Whitman, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.4 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.41546, 0.909571, 0.008543), Vector: |
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Components
#1: Protein | Mass: 8550.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: INACTIVATED BY HEPES AND BENZOIC ACID / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-BEZ / | #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.8 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PROTEIN: 25MG/ML IN 50MM HEPES, PH 7.3, 4 CELCIUS SITTING DROP: MIX 15UL PROTEIN WITH 5UL 40% SODIUM CITRATE PH 6.5 | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→25 Å / Num. obs: 35377 / % possible obs: 87.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 1 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.8 / % possible all: 33 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 156715 |
Reflection shell | *PLUS % possible obs: 33 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 8.7 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→25 Å
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Refinement | *PLUS Lowest resolution: 25 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 1.39 Å / Rfactor Rfree: 0.255 / Num. reflection Rfree: 36 / Rfactor Rwork: 0.226 / Num. reflection Rwork: 1343 / Total num. of bins used: 30 |