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- PDB-9i32: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in ... -

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Basic information

Entry
Database: PDB / ID: 9i32
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with isobutanoyl-CoA
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer / isobutanoyl-CoA / isobutanol
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
: / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III
Similarity search - Domain/homology
ISOBUTYRYL-COENZYME A / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMojanaga, O.O. / Acharya, K.R. / Lloyd, M.D.
Funding supportBotswana, 1items
OrganizationGrant numberCountry
Other governmentBotswana
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Molecular basis of acyl-CoA ester recognition by alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis.
Authors: Mojanaga, O.O. / Woodman, T.J. / Lloyd, M.D. / Acharya, K.R.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,37724
Polymers468,32612
Non-polymers10,05112
Water37,0212055
1
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7294
Polymers78,0542
Non-polymers1,6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-82 kcal/mol
Surface area27170 Å2
2
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7294
Polymers78,0542
Non-polymers1,6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-83 kcal/mol
Surface area27240 Å2
3
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7294
Polymers78,0542
Non-polymers1,6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-82 kcal/mol
Surface area27230 Å2
4
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7294
Polymers78,0542
Non-polymers1,6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-81 kcal/mol
Surface area27180 Å2
5
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7294
Polymers78,0542
Non-polymers1,6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-85 kcal/mol
Surface area27120 Å2
6
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7294
Polymers78,0542
Non-polymers1,6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-83 kcal/mol
Surface area27180 Å2
Unit cell
Length a, b, c (Å)276.488, 276.488, 390.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-581-

HOH

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Components

#1: Protein
Alpha-methylacyl-CoA racemase / AMACR / MtMCR


Mass: 39027.125 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mcr, Rv1143
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O06543, alpha-methylacyl-CoA racemase
#2: Chemical
ChemComp-CO6 / ISOBUTYRYL-COENZYME A / IB-CO6


Mass: 837.624 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C25H42N7O17P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2055 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.01 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953731 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 1.94→225.58 Å / Num. obs: 546383 / % possible obs: 100 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.046 / Net I/σ(I): 12.5
Reflection shellResolution: 10.63→225.58 Å / Redundancy: 26.1 % / Rmerge(I) obs: 0.033 / Mean I/σ(I) obs: 61.8 / Num. unique obs: 3635 / CC1/2: 1 / Rpim(I) all: 0.006 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→225.579 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.176 / SU B: 4.258 / SU ML: 0.113 / Average fsc free: 0.9493 / Average fsc work: 0.9588 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2384 27491 5.032 %
Rwork0.2071 518791 -
all0.209 --
obs-546282 99.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.588 Å2
Baniso -1Baniso -2Baniso -3
1-0.153 Å2-0 Å20 Å2
2--0.153 Å2-0 Å2
3----0.306 Å2
Refinement stepCycle: LAST / Resolution: 1.94→225.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32587 0 636 2055 35278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01234087
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631801
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.65446460
X-RAY DIFFRACTIONr_angle_other_deg0.5231.57573012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90354310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.7685348
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.017512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.315105153
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.57101503
X-RAY DIFFRACTIONr_chiral_restr0.0770.25034
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0241562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027854
X-RAY DIFFRACTIONr_nbd_refined0.2230.27447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.230863
X-RAY DIFFRACTIONr_nbtor_refined0.1810.216828
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.218095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.22059
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.213
X-RAY DIFFRACTIONr_nbd_other0.1510.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_mcbond_it3.9653.75817270
X-RAY DIFFRACTIONr_mcbond_other3.9643.75817269
X-RAY DIFFRACTIONr_mcangle_it5.7076.73721570
X-RAY DIFFRACTIONr_mcangle_other5.7076.73821571
X-RAY DIFFRACTIONr_scbond_it4.3163.99116817
X-RAY DIFFRACTIONr_scbond_other4.3163.99116818
X-RAY DIFFRACTIONr_scangle_it6.3057.20724890
X-RAY DIFFRACTIONr_scangle_other6.3047.20724891
X-RAY DIFFRACTIONr_lrange_it8.24234.84838779
X-RAY DIFFRACTIONr_lrange_other8.23434.61838402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.94-1.990.34719560.333382460.334402210.9080.9199.95280.337
1.99-2.0450.32920190.308371310.309391590.9240.93199.9770.309
2.045-2.1040.33218620.304361670.306380450.9210.93299.95790.304
2.104-2.1690.32218680.295351390.296370120.9340.94299.98650.289
2.169-2.240.29318050.266340730.267358860.9430.95499.97770.253
2.24-2.3190.28916920.256330240.258347280.9440.95799.96540.239
2.319-2.4060.27915700.242319750.244335490.9490.96399.98810.22
2.406-2.5040.27116560.231305990.233322580.9540.96899.99070.207
2.504-2.6160.2615680.221294130.223309830.9580.9799.99350.198
2.616-2.7430.2715870.218280150.221296060.9540.97199.98650.194
2.743-2.8920.25414710.223267500.224282230.9590.9799.99290.197
2.892-3.0670.2613530.214254090.217267630.9580.97399.99630.194
3.067-3.2790.25312390.224238820.226251260.9590.9799.98010.206
3.279-3.5420.24611780.214222450.215234270.9650.97599.98290.199
3.542-3.880.21211200.182204700.184215910.9750.98399.99540.171
3.88-4.3370.199590.154186380.155195970.9790.9871000.143
4.337-5.0080.1638440.138165240.14173680.9850.9891000.129
5.008-6.1330.1827770.151139750.153147520.9850.9891000.143
6.133-8.670.1686210.149108900.151115130.9850.98999.98260.142
8.67-225.5790.1593460.14162250.14265810.9880.96899.84810.138

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