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Yorodumi- PDB-2v2b: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2b | ||||||
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Title | L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E117S- E192A-K248G-R253A-E254A) | ||||||
Components | RHAMNULOSE-1-PHOSPHATE ALDOLASE | ||||||
Keywords | LYASE / ZINC ENZYME / METAL-BINDING / SURFACE MUTATION / 2-KETOSE DEGRADATION / PROTEIN-PROTEIN INTERFACE / ALDOLASE / CLASS II / RARE SUGAR / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONE PHOSPHATE / BACTERIAL L-RHAMNOSE METABOLISM / RHAMNOSE METABOLISM / PROTEIN ENGINEERING / DOMAIN MOTION FOR MECHANICAL SUPPORT OF CATALYSIS | ||||||
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: 1.5 Å | ||||||
Authors | Grueninger, D. / Schulz, G.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Antenna Domain Mobility and Enzymatic Reaction of L-Rhamnulose-1-Phosphate Aldolase. Authors: Grueninger, D. / Schulz, G.E. #1: 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. #2: 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 | 2v2b.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2b.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2b ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2b | HTTPS FTP |
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-Related structure data
Related structure data | 2v29C 2v2aC 1ojrS C: citing same article (ref.) S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29858.057 Da / Num. of mol.: 1 / 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, 222 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-PGR / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 117 TO SER 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: 2.7 Å3/Da / Density % sol: 54.5 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 40% (V/V) 1,2-PROPANEDIOL, 50 MM CA ACETATE, 100 MM ACETATE BUFFER (PH 4.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90504 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90504 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 44912 / % possible obs: 87.9 % / Observed criterion σ(I): 2.72 / Redundancy: 3.93 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.05 |
Reflection shell | Resolution: 1.5→1.56 Å / Redundancy: 2.51 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.72 / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJR Resolution: 1.5→36.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.478 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→36.35 Å
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Refine LS restraints |
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