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Yorodumi- PDB-3kx6: Crystal structure of fructose-1,6-bisphosphate aldolase from Babe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kx6 | ||||||
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Title | Crystal structure of fructose-1,6-bisphosphate aldolase from Babesia bovis at 2.1A resolution | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald Biostructures / Babesia bovis / fructose-1 / 6-bisphosphate aldolase / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process Similarity search - Function | ||||||
Biological species | Babesia bovis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of fructose-1,6-bisphosphate aldolase from Babesia bovis at 2.1A resolution Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T.E. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kx6.cif.gz | 284.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kx6.ent.gz | 228.6 KB | Display | PDB format |
PDBx/mmJSON format | 3kx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/3kx6 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/3kx6 | HTTPS FTP |
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-Related structure data
Related structure data | 2pc4S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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: 41285.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Babesia bovis (eukaryote) / Strain: T2BO / Gene: BBOV_IV000790 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7AV51, fructose-bisphosphate aldolase #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-EDO / | #5: 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: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: EBS CRYO SCREEN H12: 50% PEG 200, 100MM PHOSPHATE/CITRATE PH 4.2, 200MM NACL; BABOA.00974.A AT 30MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.975484 / Wavelength: 0.975484 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975484 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 100767 / Num. obs: 99984 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 33.47 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 5.1 / Num. unique all: 7365 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2PC4 modified with CCP4 program CHAINSAW Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.386 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, tls / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.142 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.15 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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