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Yorodumi- PDB-1lbx: Crystal Structure of a ternary complex of dual activity FBPase/IM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lbx | ||||||
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Title | Crystal Structure of a ternary complex of dual activity FBPase/IMPase (AF2372) from Archaeoglobus fulgidus with Calcium ions and D-myo-Inositol-1-Phosphate | ||||||
Components | fructose 1,6-bisphosphatase/inositol monophosphatase | ||||||
Keywords | HYDROLASE / dual activity / FBPase / IMPase / archaeal phosphatase / ternary complex with metal and substrate | ||||||
Function / homology | Function and homology information inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / signal transduction / metal ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Stieglitz, K.A. / Johnson, K.A. / Yang, H. / Roberts, M.F. / Seaton, B.A. / Head, J.F. / Stec, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of a dual activity IMPase/FBPase (AF2372) from Archaeoglobus fulgidus. The story of a mobile loop. Authors: Stieglitz, K.A. / Johnson, K.A. / Yang, H. / Roberts, M.F. / Seaton, B.A. / Head, J.F. / Stec, B. #1: Journal: Biochemistry / Year: 2001 Title: Crystal structure and catalytic mechanism of the MJ0109 gene product: a bifunctional enzyme with inositol monophosphatase and fructose 1,6-bisphosphatase activities. Authors: Johnson, K.A. / Chen, L. / Yang, H. / Roberts, M.F. / Stec, B. | ||||||
History |
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Remark 999 | SEQUENCE THIS SEQUENCE IS ANNOTATED IN THE PIR ENTRY D69546 AS SUHB ANALOGUE, WHICH WAS BASED ON ...SEQUENCE THIS SEQUENCE IS ANNOTATED IN THE PIR ENTRY D69546 AS SUHB ANALOGUE, WHICH WAS BASED ON SEQUENCE HOMOLOGIES, NOT BIOCHEMICAL ASSAYS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lbx.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lbx.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/1lbx ftp://data.pdbj.org/pub/pdb/validation_reports/lb/1lbx | HTTPS FTP |
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-Related structure data
Related structure data | 1lbvC 1lbwC 1lbyC 1lbzC 1dk4S C: citing same article (ref.) S: Starting model for refinement |
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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: 28002.838 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF2372 / Production host: Escherichia coli (E. coli) References: UniProt: O30298, fructose-bisphosphatase, inositol-phosphate phosphatase #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 2.07 Å3/Da / Density % sol: 40.66 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, ammonium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2001 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 17131 / Num. obs: 15657 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1768 / % possible all: 98.1 |
Reflection | *PLUS % possible obs: 94.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.136 |
Reflection shell | *PLUS % possible obs: 92.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DK4 Resolution: 2.4→20 Å / Num. parameters: 16243 / Num. restraintsaints: 16381 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: SHELXL CONJUGATED GRADIENT
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Solvent computation | Solvent model: moews & kretsinger | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.201 / Rfactor obs: 0.182 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.182 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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