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Yorodumi- PDB-2v9n: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v9n | ||||||
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Title | L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F- 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: 1.4 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. / Koetter, J.W. / 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 | 2v9n.cif.gz | 488.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v9n.ent.gz | 401.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v9n_validation.pdf.gz | 509 KB | Display | wwPDB validaton report |
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Full document | 2v9n_full_validation.pdf.gz | 522.3 KB | Display | |
Data in XML | 2v9n_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 2v9n_validation.cif.gz | 80.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v9n ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v9n | HTTPS FTP |
-Related structure data
Related structure data | 2uyuC 2uyvC 2v7gC 2v9eC 2v9fC 2v9gC 2v9iC 2v9lC 2v9mC 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 274 / Label seq-ID: 1 - 274
NCS oper: (Code: given Matrix: (0.2614, 0.03225, 0.9647), Vector: |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 30192.467 Da / Num. of mol.: 4 / 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 , 6 types, 1241 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CIT / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-PGO / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 88 TO PHE ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ...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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 4.9 Details: 25% (V/V) 1,2-PROPANEDIOL, 10% (V/V) GLYCEROL, 5% (W/V) PEG 3000, PHOSPHATE-CITRATE BUFFER (0.1M, PH 4.2) |
-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 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: 1.4→51 Å / Num. obs: 268317 / % possible obs: 91 % / Observed criterion σ(I): 2.88 / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.25 |
Reflection shell | Highest resolution: 1.4 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.88 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJR Resolution: 1.4→51.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.848 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.057 / 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: 7.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→51.03 Å
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Refine LS restraints |
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