+Open data
-Basic information
Entry | Database: PDB / ID: 1gt7 | ||||||
---|---|---|---|---|---|---|---|
Title | L-rhamnulose-1-phosphate aldolase from Escherichia coli | ||||||
Components | RHAMNULOSE-1-PHOSPHATE ALDOLASE | ||||||
Keywords | LYASE / ALDOLASE (LYASE) / CLASS II / ZINC ENZYME / BACTERIAL L- RHAMNOSE METABOLISM / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.7 Å | ||||||
Authors | Kroemer, M. / Schulz, G.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 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: Journal: J.Mol.Biol. / Year: 2000 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gt7.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gt7.ent.gz | 920 KB | Display | PDB format |
PDBx/mmJSON format | 1gt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/1gt7 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/1gt7 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | THE PROTEIN IS ACTIVE AS TETRAMER |
-Components
#1: Protein | Mass: 30174.404 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKK223-3 (GEN RHAD) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 References: UniProt: P32169, rhamnulose-1-phosphate aldolase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PGH / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.907 |
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 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR / Resolution: 2.7→44 Å / SU B: 11.6 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.31 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.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44 Å
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 44 Å / Rfactor obs: 0.233 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |