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- PDB-2v9f: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v9f | ||||||
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Title | L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A- K248W-A273S) | ||||||
![]() | RHAMNULOSE-1-PHOSPHATE ALDOLASE | ||||||
![]() | LYASE / ENTROPY INDEX / METAL-BINDING / OLIGOMERIZATION / ZINC / ALDOLASE / CLASS II / CYTOPLASM / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPH BACTERIAL L-RHAMNOSE METABOLISM / INTERFACE DESIGN / SURFACE MUTATION / 2-KETOSE DEGRADATION / PROTEIN-PROTEIN INTERFACE / RARE SUGAR / AGGREGATION / ZINC ENZYME / FIBRILLATION / RHAMNOSE METABOLISM / PROTEIN ENGINEERING | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Grueninger, D. / Schulz, G.E. | ||||||
![]() | ![]() Title: Designed Protein-Protein Association. Authors: Grueninger, D. / Treiber, N. / Ziegler, M.O.P. / Koetter, J.W.A. / Schulze, M.-S. / Schulz, G.E. #1: ![]() Title: Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase Authors: Kroemer, M. / Merkel, I. / Schulz, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2uyuC ![]() 2uyvC ![]() 2v7gC ![]() 2v9eC ![]() 2v9gC ![]() 2v9iC ![]() 2v9lC ![]() 2v9mC ![]() 2v9nC ![]() 2v9oC ![]() 2v9uC ![]() 1ojrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given) |
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Components
#1: Protein | Mass: 30189.400 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32169, rhamnulose-1-phosphate aldolase | ||||||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 248 TO TRP ...ENGINEERED | Sequence details | RHAD_ECOLI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.3 % / Description: NONE |
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Crystal grow | pH: 7.2 Details: 40% (V/V) PEG 400, 0.1 M HEPES (PH 7.5), 0.2 M CALCIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 17559 / % possible obs: 91.6 % / Observed criterion σ(I): 5 / Redundancy: 7.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.68 |
Reflection shell | Highest resolution: 2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.05 / % possible all: 49.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OJR Resolution: 2.1→24.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3133262.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.7267 Å2 / ksol: 0.389476 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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