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Yorodumi- PDB-6ayy: Crystal structure of Apo fructose-1,6-bisphosphatase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ayy | ||||||
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Title | Crystal structure of Apo fructose-1,6-bisphosphatase from Mycobacterium tuberculosis | ||||||
Components | Fructose-1,6-bisphosphatase class 2 | ||||||
Keywords | HYDROLASE / Fructose-1 / 6-bisphosphatase / gluconeogenesis / Class II phosphatase | ||||||
Function / homology | Function and homology information glycerol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å | ||||||
Authors | Abad-Zapatero, C. / Wolf, N. / Gutka, H.J. / Movahedzadeh, F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition. Authors: Wolf, N.M. / Gutka, H.J. / Movahedzadeh, F. / Abad-Zapatero, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ayy.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayy.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ayy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ayy_validation.pdf.gz | 482.9 KB | Display | wwPDB validaton report |
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Full document | 6ayy_full_validation.pdf.gz | 499.9 KB | Display | |
Data in XML | 6ayy_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 6ayy_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayy ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayy | HTTPS FTP |
-Related structure data
Related structure data | 6ayuC 6ayvSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36660.430 Da / Num. of mol.: 2 / Fragment: UNP residues 35-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: glpX, MT1131 / Plasmid: pET15b / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P9WN20, fructose-bisphosphatase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-UNX / | #4: Chemical | ChemComp-CIT / | #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: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M ammonium citrate, 1% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 23145 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.017 / Rsym value: 0.079 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 22.1 % / Rmerge(I) obs: 1.806 / Mean I/σ(I) obs: 1.706 / Num. unique all: 1074 / CC1/2: 0.672 / Rpim(I) all: 0.456 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AYV Resolution: 2.601→19.95 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.601→19.95 Å
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Refine LS restraints |
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LS refinement shell |
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