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Yorodumi- PDB-6ayv: Crystal structure of fructose-1,6-bisphosphatase T84A from Mycoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ayv | ||||||
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Title | Crystal structure of fructose-1,6-bisphosphatase T84A from Mycobacterium tuberculosis | ||||||
Components | Fructose-1,6-bisphosphatase class 2 | ||||||
Keywords | HYDROLASE / Fructose-1 / 6-bisphosphatase / gluconeogenesis / Class II phosphatase / Mycobacterium tuberculosis | ||||||
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: 2.3 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 | 6ayv.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayv.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ayv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayv ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayv | HTTPS FTP |
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-Related structure data
Related structure data | 6ayuC 6ayyC 3d1rS 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 36630.406 Da / Num. of mol.: 2 / Fragment: UNP residues 35-362 / Mutation: T84A 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: Sugar | |
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-Non-polymers , 4 types, 318 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MLI / | #6: 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: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.4 M sodium malonate pH 6.0 |
-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: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 33376 / % possible obs: 100 % / Redundancy: 23.7 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.026 / Rsym value: 0.125 / Net I/σ(I): 55 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 21.4 % / Rmerge(I) obs: 2.314 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1613 / CC1/2: 0.691 / Rpim(I) all: 0.517 / Rsym value: 2.314 / Χ2: 0.95 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3d1r Resolution: 2.3→38.768 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / 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: 2.3→38.768 Å
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Refine LS restraints |
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LS refinement shell |
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