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Yorodumi- PDB-1j4e: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j4e | ||||||
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Title | FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTRATE DIHYDROXYACETONE PHOSPHATE | ||||||
Components | FRUCTOSE-BISPHOSPHATE ALDOLASE A | ||||||
Keywords | LYASE / ALDOLASE / GLYCOLYSIS | ||||||
Function / homology | Function and homology information negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Choi, K.H. / Shi, J. / Hopkins, C.E. / Tolan, D.R. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate. Authors: Choi, K.H. / Shi, J. / Hopkins, C.E. / Tolan, D.R. / Allen, K.N. #1: Journal: Biochemistry / Year: 1999 Title: Structure of a Fructose-1,6-(Bis)Phosphate Aldolase Liganded to its Natural Substrate in a Cleavage-Defective Mutant at 2.3 A Authors: Choi, K.H. / Mazurkie, A.S. / Morris, A.J. / Utheza, D. / Tolan, D.R. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j4e.cif.gz | 240.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j4e.ent.gz | 198.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j4e_validation.pdf.gz | 477.2 KB | Display | wwPDB validaton report |
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Full document | 1j4e_full_validation.pdf.gz | 513.2 KB | Display | |
Data in XML | 1j4e_validation.xml.gz | 52 KB | Display | |
Data in CIF | 1j4e_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/1j4e ftp://data.pdbj.org/pub/pdb/validation_reports/j4/1j4e | HTTPS FTP |
-Related structure data
Related structure data | 6aldS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39135.418 Da / Num. of mol.: 4 / Mutation: C72A, C239A, C289A, C338A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / Plasmid: PPB14 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P00883, fructose-bisphosphate aldolase #2: Chemical | ChemComp-13P / #3: 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: 2.18 Å3/Da / Density % sol: 43.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Detector: CCD / Date: Mar 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 35634 / % possible obs: 86 % / Redundancy: 3 % / Rsym value: 0.034 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2 % / Mean I/σ(I) obs: 10 / Rsym value: 0.22 / % possible all: 60 |
Reflection | *PLUS Lowest resolution: 9999 Å / % possible obs: 86 % / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 60 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 10 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6ALD Resolution: 2.65→100 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: mlf Details: WE HAVE ALTERED PROTEIN_REP.PARAM AND PROTEIN.TOP TO INCLUDE THE COVALENTLY MODIFIED LYSINE
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Displacement parameters | Biso mean: 31.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.341 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.67 Å / Total num. of bins used: 50
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 9.5 % |