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Yorodumi- PDB-2v9m: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v9m | ||||||
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Title | L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A87M- T109F-E192A) | ||||||
Components | RHAMNULOSE-1-PHOSPHATE ALDOLASE | ||||||
Keywords | 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 | 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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Grueninger, D. / Schulz, G.E. | ||||||
Citation | Journal: Science / Year: 2008 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: Journal: Biochemistry / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v9m.cif.gz | 280.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v9m.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v9m_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 2v9m_full_validation.pdf.gz | 480.6 KB | Display | |
Data in XML | 2v9m_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 2v9m_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v9m ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v9m | HTTPS FTP |
-Related structure data
Related structure data | 2uyuC 2uyvC 2v7gC 2v9eC 2v9fC 2v9gC 2v9iC 2v9lC 2v9nC 2v9oC 2v9uC 1ojrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30222.557 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 References: UniProt: P32169, rhamnulose-1-phosphate aldolase |
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-Non-polymers , 5 types, 826 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-CIT / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 7.4 / Details: 40% (V/V) ETHYLENE GLYCOL, 0.1 M TRIS (PH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 14, 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: 1.3→20 Å / Num. obs: 161435 / % possible obs: 99.9 % / Redundancy: 8.38 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.88 |
Reflection shell | Highest resolution: 1.3 Å / Redundancy: 8.26 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.39 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJR Resolution: 1.3→20 Å / Num. parameters: 50193 / Num. restraintsaints: 65952 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Refine analyze | Num. disordered residues: 84 / Occupancy sum hydrogen: 4251.05 / Occupancy sum non hydrogen: 5104.99 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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