[English] 日本語
Yorodumi- PDB-1dzu: L-Fuculose-1-Phosphate Aldolase from Escherichia coli Mutant T26A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dzu | ||||||
---|---|---|---|---|---|---|---|
Title | L-Fuculose-1-Phosphate Aldolase from Escherichia coli Mutant T26A | ||||||
Components | L-fuculose phosphate aldolase | ||||||
Keywords | LYASE (ALDEHYDE) / ALDOLASE (CLASS II) / BACTERIAL L-FUCOSE METABOLISM / CLEAVAGE OF L-FUCULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE / MUTANT STRUCTURE | ||||||
Function / homology | Function and homology information arabinose catabolic process / L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / D-arabinose catabolic process / L-fucose catabolic process / pentose catabolic process / aldehyde-lyase activity / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.09 Å | ||||||
Authors | Joerger, A.C. / Schulz, G.E. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Catalytic Action of Fuculose 1-Phosphate Aldolase (Class II) as Derived from Structure-Directed Mutagenesis Authors: Joerger, A.C. / Gosse, C. / Fessner, W.-D. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Catalytic Mechanism of the Metal-Dependent Fuculose Aldolase from Escherichia Coli as Derived from the Structure Authors: Dreyer, M.K. / Schulz, G.E. #2: Journal: J.Mol.Biol. / Year: 1993 Title: The Spatial Structure of the Class II L-Fuculose-1-Phosphate Aldolase from Escherichia Coli Authors: Dreyer, M.K. / Schulz, G.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dzu.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dzu.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dzu_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dzu_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 1dzu_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1dzu_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dzu ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dzu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 23775.293 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: T26A SUBSTITUTION PERFORMED WITH PHOSPHOROTHIOATE METHOD USING M13MP19 Gene: fucA, fucA_1, fucA_2, A9R57_06860, ACU57_24310, AM464_05705, AUQ13_17640, BANRA_01321, BANRA_04164, BANRA_04304, BHS87_15835, BJJ90_05160, BUE81_06870, BvCms12BK_05168, BvCms2454_02072, ...Gene: fucA, fucA_1, fucA_2, A9R57_06860, ACU57_24310, AM464_05705, AUQ13_17640, BANRA_01321, BANRA_04164, BANRA_04304, BHS87_15835, BJJ90_05160, BUE81_06870, BvCms12BK_05168, BvCms2454_02072, BvCmsHHP001_01136, BvCmsHHP056_02000, BvCmsKKP061_04411, BvCmsKSP011_02414, BvCmsKSP024_03378, BvCmsKSP026_00082, BvCmsKSP040_03336, BvCmsKSP045_02228, BvCmsKSP067_03660, BvCmsNSNP027_02922, BvCmsNSP047_01577, BvCmsSINP012_00041, BW690_04870, C4J69_11555, C9E25_03225, CV83915_03318, D2185_02685, D3821_11040, D3Y67_10455, D9D20_04550, D9E35_20280, D9H68_17240, DP258_16175, E5M00_06120, EAI52_12600, EC3234A_48c01090, ECTO6_01047, EEP23_13950, EFB45_09210, EL75_0893, EL79_0895, EL80_0898, EPS71_16910, EPT01_16955, ERS085365_02448, ERS085366_03061, ERS085416_02919, ERS139211_02051, ERS150873_02024, EXX32_11695, EXX39_16005, EXX71_16135, HmCms184_04796, NCTC11181_03256, NCTC13462_04786, NCTC8500_01060, NCTC9037_01222, NCTC9045_01197, NCTC9058_00868, NCTC9062_02153, NCTC9706_03275, RK56_023265, SAMEA3472047_00318, SAMEA3472080_03134, SAMEA3484427_03277, SAMEA3484429_03394, SAMEA3752559_02974, SAMEA3753300_01128, SK85_03044, WR15_06195 Plasmid: PKKFA2-T26A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 105 References: UniProt: A0A037YR34, UniProt: P0AB87*PLUS, L-fuculose-phosphate aldolase | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-BME / | #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Compound details | CHAIN P ENGINEERED | Sequence details | THE C-TERMINAL RESIDUES 210-215 ARE DISORDERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: CRYSTALS GROWN FROM AMMONIUM SULFATE AT PH 8.0,VAPOUR DIFFUSION, HANGING DROP, CONDITIONS CLOSE TO THE ONES REPORTED FOR THE WILD-TYPE, SEE PDB ID 1FUA FOR FURTHER DETAILS |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS X-1000 CCD / Detector: CCD / Date: Feb 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→10 Å / Num. obs: 10121 / % possible obs: 87 % / Redundancy: 3.1 % / Rsym value: 0.066 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.15 / % possible all: 78 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 78 % / Num. unique obs: 822 / Rmerge(I) obs: 0.15 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 2.09→10 Å / SU B: 2.9 / SU ML: 0.07 / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|