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- PDB-2yim: The enolisation chemistry of a thioester-dependent racemase: the ... -

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Basic information

Entry
Database: PDB / ID: 2yim
TitleThe enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue
ComponentsPROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
KeywordsISOMERASE / METHYL-COA RACEMASE / TRANSITION STATE / MOLECULAR DYNAMICS / QM/MM / OXYANION HOLE
Function / homology
Function and homology information


alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / acyl-CoA metabolic process / lipid metabolic process / protein homodimerization activity
Similarity search - Function
: / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich ...: / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-METHYLACETOACETYL COA / PHOSPHATE ION / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsSharma, S. / Bhaumik, P. / Venkatesan, R. / Hiltunen, J.K. / Conzelmann, E. / Juffer, A.H. / Wierenga, R.K.
Citation
Journal: J Phys Chem B / Year: 2012
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: Journal: J.Mol.Biol. / Year: 2007
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
DepositionMay 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
B: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
C: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
D: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,00015
Polymers154,8914
Non-polymers4,10911
Water32,7511818
1
A: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
B: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4547
Polymers77,4462
Non-polymers2,0085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-89 kcal/mol
Surface area24840 Å2
MethodPISA
2
C: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
D: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5468
Polymers77,4462
Non-polymers2,1016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-84.9 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.590, 80.170, 118.880
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE ) / ALPHA-METHYLACYL-COA RACEMASE


Mass: 38722.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 2-METHYLACETOACETYL COA / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET3ALPHA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O06543, alpha-methylacyl-CoA racemase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MC4 / 2-METHYLACETOACETYL COA


Mass: 864.626 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H41N7O18P3S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1818 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.96 % / Description: NONE
Crystal growpH: 7 / Details: 1.52 M AMMONIUM PHOSPHATE PH 7.0, 10 MM BACL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GCE

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 16290 5 %RANDOM
Rwork0.18615 ---
obs0.18707 306469 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.04 Å2
2--0.1 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.41→118.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10731 0 260 1818 12809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.98516523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88151618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84623.08539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.743151891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.01115120
X-RAY DIFFRACTIONr_chiral_restr0.0730.21766
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219450
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3761.57432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.703211948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96534596
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5744.54484
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 1183 -
Rwork0.29 22157 -
obs--96.87 %

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