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Open data
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Basic information
Entry | Database: PDB / ID: 1gt7 | ||||||
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Title | L-rhamnulose-1-phosphate aldolase from Escherichia coli | ||||||
![]() | RHAMNULOSE-1-PHOSPHATE ALDOLASE | ||||||
![]() | LYASE / ALDOLASE (LYASE) / CLASS II / ZINC ENZYME / BACTERIAL L- RHAMNOSE METABOLISM / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE | ||||||
Function / homology | ![]() rhamnulose-1-phosphate aldolase / rhamnulose-1-phosphate aldolase activity / rhamnose catabolic process / pentose catabolic process / aldehyde-lyase activity / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kroemer, M. / Schulz, G.E. | ||||||
![]() | ![]() Title: The Structure of L-Rhamnulose-1-Phosphate Aldolase (Class II) Solved by Low-Resolution Sir Phasing and 20-Fold Ncs Averaging Authors: Kroemer, M. / Schulz, G.E. #1: ![]() Title: Structures of L-Fuculose-1-Phosphate Aldolase Mutants Outlining Motions During Catalysis Authors: Joerger, A.C. / Mueller-Dieckmann, C. / Schulz, G.E. #2: Journal: J.Bacteriol. / Year: 1993 Title: Sequencing and Characterization of a Gene Cluster Encoding the Enzymes for L-Rhamnose Metabolism in Escherichia Coli Authors: Moralejo, P. / Egan, S.M. / Hidalgo, E. / Aguilar, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 920 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626.4 KB | Display | ![]() |
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Full document | ![]() | 795 KB | Display | |
Data in XML | ![]() | 252.9 KB | Display | |
Data in CIF | ![]() | 323.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE PROTEIN IS ACTIVE AS TETRAMER |
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Components
#1: Protein | Mass: 30174.404 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32169, rhamnulose-1-phosphate aldolase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PGH / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: HANGING DROP CONTAINED 5 MG/ML PROTEIN, 5 MM PGH, 0.9 M SODIUM FORMATE, 5 MM MERCAPTOETHANOL, 0.5 MM ZNCL2 AND 0.1 M SODIUM ACETATE (PH 4.6). RESERVOIR CONTAINED 1.8 M SODIUM FORMATE, 5 MM ...Details: HANGING DROP CONTAINED 5 MG/ML PROTEIN, 5 MM PGH, 0.9 M SODIUM FORMATE, 5 MM MERCAPTOETHANOL, 0.5 MM ZNCL2 AND 0.1 M SODIUM ACETATE (PH 4.6). RESERVOIR CONTAINED 1.8 M SODIUM FORMATE, 5 MM MERCAPTOETHANOL AND 0.1 M SODIUM ACETATE (PH 4.6) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.907 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45 Å / Num. obs: 207606 / % possible obs: 90.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / % possible all: 89.8 |
Reflection | *PLUS Lowest resolution: 45 Å / % possible obs: 91 % / Num. measured all: 611276 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 90 % / Rmerge(I) obs: 0.37 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE TWENTYFOLD NON-CRYSTALLOGRAPHIC SYMMETRY WAS ALWAYS TIGHTLY RESTRAINED ARRANGING THE TWENTY PROTEIN CHAINS IN ONE NCS GROUP, AND THE TWENTY ZN IONS, PGH MOLECULES AND WATER MOLECULE ...Details: THE TWENTYFOLD NON-CRYSTALLOGRAPHIC SYMMETRY WAS ALWAYS TIGHTLY RESTRAINED ARRANGING THE TWENTY PROTEIN CHAINS IN ONE NCS GROUP, AND THE TWENTY ZN IONS, PGH MOLECULES AND WATER MOLECULE CHAINS AS A SECOND NCS GROUP. THE GEOMETRY AND VDW DISTANCES OF SOME SURFACE RESIDUES WERE THEREFORE DISTURBED DUE TO CLASHES IN CRYSTAL CONTACTS THAT DO NOT FOLLOW THE OVERALL NON-CRYSTALLOGRAPHIC SYMMETRY.
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Refinement step | Cycle: LAST / Resolution: 2.7→44 Å
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Refinement | *PLUS Lowest resolution: 44 Å / Rfactor obs: 0.233 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |