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- PDB-3ll4: Structure of the H13A mutant of Ykr043C in complex with fructose-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ll4 | ||||||
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Title | Structure of the H13A mutant of Ykr043C in complex with fructose-1,6-bisphosphate | ||||||
![]() | Uncharacterized protein YKR043C | ||||||
![]() | HYDROLASE / fructose-1 / 6-bisphosphatase / 1 / 6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Ykr043C / Saccharomyces cerevisiae / metal-independent / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() sedoheptulose-bisphosphatase / sedoheptulose-bisphosphatase activity / ribose phosphate biosynthetic process / oxidoreductase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Singer, A. / Xu, X. / Cui, H. / Dong, A. / Stogios, P.J. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae. Authors: Kuznetsova, E. / Xu, L. / Singer, A. / Brown, G. / Dong, A. / Flick, R. / Cui, H. / Cuff, M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | 92.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1000 KB | Display | ![]() |
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Full document | ![]() | 1005.2 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f3kSC ![]() 3lg2C S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 33427.434 Da / Num. of mol.: 2 / Mutation: H13A Source method: isolated from a genetically manipulated source Details: no TEV cleavage, but limiting amounts of trypsin added during crystallization Source: (gene. exp.) ![]() ![]() Strain: S288C / Gene: YKR043C / Plasmid: P15TvLic / Production host: ![]() ![]() #2: Sugar | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: resevoir of 0.1M Sodium Hepes ph7.5, 10% isopropanol and 20% PEG4K. 0.03 mg/ml trypsin was added to the protein prior to crystallization setup. Crystals were washed in well solution, then ...Details: resevoir of 0.1M Sodium Hepes ph7.5, 10% isopropanol and 20% PEG4K. 0.03 mg/ml trypsin was added to the protein prior to crystallization setup. Crystals were washed in well solution, then soaked in well solution plus 12% Glycerol and 0.1M fructose 1,6 bis-phosphate at room temperature for 10 minutes prior to flash-freezing in liquid N2, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 14, 2009 / Details: mirrors |
Radiation | Monochromator: VariMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→31.39 Å / Num. all: 25683 / Num. obs: 25181 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 21.28 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1215 / % possible all: 89.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3F3K molecule A Resolution: 2.49→31.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.829 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.29 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→31.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2096 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.487→2.551 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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