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- PDB-2yim: The enolisation chemistry of a thioester-dependent racemase: the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yim | ||||||
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Title | The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue | ||||||
![]() | PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE ) | ||||||
![]() | ISOMERASE / METHYL-COA RACEMASE / TRANSITION STATE / MOLECULAR DYNAMICS / QM/MM / OXYANION HOLE | ||||||
Function / homology | ![]() alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / acyl-CoA metabolic process / bile acid metabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, S. / Bhaumik, P. / Venkatesan, R. / Hiltunen, J.K. / Conzelmann, E. / Juffer, A.H. / Wierenga, R.K. | ||||||
![]() | ![]() Title: The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed Qm/Mm Calculations. Authors: Sharma, S. / Bhaumik, P. / Schmitz, W. / Venkatesan, R. / Hiltunen, J.K. / Conzelmann, E. / Juffer, A.H. / Wierenga, R.K. #1: ![]() Title: The Catalysis of the 1,1-Proton Transfer by Alpha-Methyl-Acyl-Coa Racemase is Coupled to a Movement of the Fatty Acyl Moiety Over a Hydrophobic, Methionine-Rich Surface. Authors: Bhaumik, P. / Schmitz, W. / Hassinen, A. / Hiltunen, J.K. / Conzelmann, E. / Wierenga, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.2 KB | Display | ![]() |
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PDB format | ![]() | 271.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 73.4 KB | Display | |
Data in CIF | ![]() | 109.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gceS S: Starting model for refinement |
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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
#1: Protein | Mass: 38722.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 2-METHYLACETOACETYL COA / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MC4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.96 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.52 M AMMONIUM PHOSPHATE PH 7.0, 10 MM BACL2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→21.3 Å / Num. obs: 322760 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.41→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GCE Resolution: 1.41→118.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.962 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.062 / 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: 15.115 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→118.84 Å
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Refine LS restraints |
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