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- PDB-2gd2: The 1,1-proton transfer reaction mechanism by alpha-methylacyl-Co... -

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Basic information

Entry
Database: PDB / ID: 2gd2
TitleThe 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety
Componentsprobable alpha-methylacyl-CoA racemase MCR
KeywordsISOMERASE / Alpha-methylacyl-CoA racemase / racemase / CoA transferase / proton transfer / Coenzyme A
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
ACETOACETYL-COENZYME A / : / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBhaumik, P. / Wierenga, R.K.
CitationJournal: 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
DepositionMar 15, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
B: probable alpha-methylacyl-CoA racemase MCR
C: probable alpha-methylacyl-CoA racemase MCR
D: probable alpha-methylacyl-CoA racemase MCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,48210
Polymers154,8914
Non-polymers3,5916
Water27,9951554
1
A: probable alpha-methylacyl-CoA racemase MCR
B: probable alpha-methylacyl-CoA racemase MCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2415
Polymers77,4462
Non-polymers1,7953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-76 kcal/mol
Surface area23980 Å2
MethodPISA
2
C: probable alpha-methylacyl-CoA racemase MCR
D: probable alpha-methylacyl-CoA racemase MCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2415
Polymers77,4462
Non-polymers1,7953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-78 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.120, 80.030, 118.620
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA2 - 392 - 39
21ALAALAPROPROBB2 - 392 - 39
31ALAALAPROPROCC2 - 392 - 39
41ALAALAPROPRODD2 - 392 - 39
52ILEILEALAALAAA45 - 28045 - 280
62ILEILEALAALABB45 - 28045 - 280
72ILEILEALAALACC45 - 28045 - 280
82ILEILEALAALADD45 - 28045 - 280
93SERSERGLUGLUAA294 - 321294 - 321
103SERSERGLUGLUBB294 - 321294 - 321
113SERSERGLUGLUCC294 - 321294 - 321
123SERSERGLUGLUDD294 - 321294 - 321
134TRPTRPGLYGLYAA326 - 360326 - 360
144TRPTRPGLYGLYBB326 - 360326 - 360
154TRPTRPGLYGLYCC326 - 360326 - 360
164TRPTRPGLYGLYDD326 - 360326 - 360

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Components

#1: Protein
probable alpha-methylacyl-CoA racemase MCR / 2-methylacyl-CoA racemase / 2-arylpropionyl-CoA epimerase


Mass: 38722.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: CAB09031 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: GenBank: 2117181, UniProt: O06543*PLUS, alpha-methylacyl-CoA racemase
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1554 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.52M Ammonium phosphate, 10mM Barium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.395 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2004 / Details: Bent mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.395 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 176396 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.3 / Num. unique all: 14090 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X74

1x74


Resolution: 1.7→19.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.702 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24988 8538 5 %RANDOM
Rwork0.20775 ---
all0.20986 161331 --
obs0.208 161331 91.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.164 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 216 1554 12486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02111336
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.96315444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91451425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5123.112511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.372151724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21415112
X-RAY DIFFRACTIONr_chiral_restr0.1230.21652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028820
X-RAY DIFFRACTIONr_nbd_refined0.2160.25910
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.21331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.266
X-RAY DIFFRACTIONr_mcbond_it1.0041.57279
X-RAY DIFFRACTIONr_mcangle_it1.404211268
X-RAY DIFFRACTIONr_scbond_it2.27334684
X-RAY DIFFRACTIONr_scangle_it3.1914.54176
Refine LS restraints NCS

Ens-ID: 1 / Number: 2555 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.165
2Bloose positional0.165
3Cloose positional0.235
4Dloose positional0.25
1Aloose thermal1.3710
2Bloose thermal1.8310
3Cloose thermal1.5310
4Dloose thermal1.4110
LS refinement shellResolution: 1.7→1.791 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.347 1126 -
Rwork0.317 21059 -
obs-14090 82.55 %

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