[English] 日本語
Yorodumi- PDB-2v2a: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2a | ||||||
---|---|---|---|---|---|---|---|
Title | L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT 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: 1.75 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: Biochemistry / Year: 2003 Title: Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase Authors: Kroemer, M. / Merkel, I. / Schulz, G.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v2a.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v2a.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v2a_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2v2a_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 2v2a_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2v2a_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2a ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2a | HTTPS FTP |
-Related structure data
Related structure data | 2v29C 2v2bC 1ojrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29900.092 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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-13P / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 248 TO GLY ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.6 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.89996 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89996 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 30749 / % possible obs: 92.6 % / Observed criterion σ(I): 11.35 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.03 |
Reflection shell | Resolution: 1.75→1.83 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 11.35 / % possible all: 44.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJR Resolution: 1.75→19.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.788 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13.02 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|