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- PDB-2v9o: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v9o | ||||||
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Title | L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A87M- T109F-E192A) | ||||||
![]() | RHAMNULOSE-1-PHOSPHATE ALDOLASE | ||||||
![]() | LYASE / ENTROPY INDEX / METAL-BINDING / OLIGOMERIZATION / ALDOLASE / CLASS II / 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 | ![]() | 125.3 KB | Display | ![]() |
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PDB format | ![]() | 97.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 459.4 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2uyuC ![]() 2uyvC ![]() 2v7gC ![]() 2v9eC ![]() 2v9fC ![]() 2v9gC ![]() 2v9iC ![]() 2v9lC ![]() 2v9mC ![]() 2v9nC ![]() 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.9939, 0.1099, -0.004256), Vector: |
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Components
#1: Protein | Mass: 30222.557 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32169, rhamnulose-1-phosphate aldolase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 87 TO MET ENGINEERED RESIDUE IN CHAIN A, THR 109 TO PHE ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.5 % / Description: NONE |
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Crystal grow | pH: 7.3 Details: 50% (V/V) ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.5), 0.2 M LITHIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45 Å / Num. obs: 47805 / % possible obs: 99.7 % / Observed criterion σ(I): 3.9 / Redundancy: 4.33 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.45 |
Reflection shell | Highest resolution: 1.95 Å / Redundancy: 4.12 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OJR Resolution: 1.95→44.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.009 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→44.95 Å
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Refine LS restraints |
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