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- PDB-9i2u: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in ... -

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Basic information

Entry
Database: PDB / ID: 9i2u
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with ibuprofenoyl-CoA
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer / ibuprofenoyl-CoA / ibuprofen
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
(S)-IBUPROFENOYL-COENZYME A / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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)479,80724
Polymers468,32612
Non-polymers11,48212
Water22,7711264
1
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9684
Polymers78,0542
Non-polymers1,9142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16230 Å2
ΔGint-75 kcal/mol
Surface area23960 Å2
MethodPISA
2
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9684
Polymers78,0542
Non-polymers1,9142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16140 Å2
ΔGint-73 kcal/mol
Surface area24180 Å2
MethodPISA
3
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9684
Polymers78,0542
Non-polymers1,9142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16270 Å2
ΔGint-74 kcal/mol
Surface area24000 Å2
MethodPISA
4
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9684
Polymers78,0542
Non-polymers1,9142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-73 kcal/mol
Surface area24080 Å2
MethodPISA
5
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9684
Polymers78,0542
Non-polymers1,9142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16070 Å2
ΔGint-73 kcal/mol
Surface area24110 Å2
MethodPISA
6
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9684
Polymers78,0542
Non-polymers1,9142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-70 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)277.033, 277.033, 390.741
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-572-

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-SFC / (S)-IBUPROFENOYL-COENZYME A / [5-(6-AMINOPURIN-9-YL)-2-[[[[3-[2-(2-(S)-2-[4-(2-METHYLPROPYL)PHENYL] PROPANOYL)-SULFANYLETHYLCARBAMOYL ETHYLCARBAMOYL]-3-HYDROXY-2,2-DIMETHYL-PROPOXY]-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXYMETHYL]-4-HYDROXY-OXOLAN-3-YL]OXYPHOSPHONIC ACID


Mass: 956.808 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H53N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1264 / 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: 4.03 Å3/Da / Density % sol: 69.5 %
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: 2.17→226 Å / Num. obs: 393535 / % possible obs: 100 % / Redundancy: 27.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.053 / Rrim(I) all: 0.282 / Net I/σ(I): 10.4
Reflection shellResolution: 11.89→226 Å / Redundancy: 25.5 % / Rmerge(I) obs: 0.041 / Mean I/σ(I) obs: 41.9 / Num. unique obs: 2661 / CC1/2: 0.996 / Rpim(I) all: 0.008 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→196.662 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.205 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.239 19705 5.008 %
Rwork0.2005 373784 -
all0.202 --
obs-393489 99.988 %
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: 51.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.159 Å20 Å2-0 Å2
2---0.159 Å2-0 Å2
3---0.317 Å2
Refinement stepCycle: LAST / Resolution: 2.17→196.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32381 0 744 1264 34389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01233960
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631791
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.8146278
X-RAY DIFFRACTIONr_angle_other_deg0.5841.74972932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19454261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.5225336
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.79212.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.656105127
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.275101492
X-RAY DIFFRACTIONr_chiral_restr0.080.25016
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0241355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027853
X-RAY DIFFRACTIONr_nbd_refined0.2230.27328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.230226
X-RAY DIFFRACTIONr_nbtor_refined0.1810.216430
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.217646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.21587
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0880.29
X-RAY DIFFRACTIONr_nbd_other0.1380.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.215
X-RAY DIFFRACTIONr_mcbond_it5.0194.94517101
X-RAY DIFFRACTIONr_mcbond_other5.0184.94517101
X-RAY DIFFRACTIONr_mcangle_it7.5448.86121337
X-RAY DIFFRACTIONr_mcangle_other7.5458.86221338
X-RAY DIFFRACTIONr_scbond_it4.975.31816859
X-RAY DIFFRACTIONr_scbond_other4.975.31916860
X-RAY DIFFRACTIONr_scangle_it7.4899.60624939
X-RAY DIFFRACTIONr_scangle_other7.4889.60624940
X-RAY DIFFRACTIONr_lrange_it9.88544.83237824
X-RAY DIFFRACTIONr_lrange_other9.944.74137624
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
2.17-2.2260.3515100.339273800.34288930.9120.91599.98960.343
2.226-2.2870.33112910.313269160.314282180.920.9399.9610.316
2.287-2.3540.3213180.294260690.296273890.9260.9499.99270.294
2.354-2.4260.31113990.276252150.278266180.9360.9599.9850.272
2.426-2.5060.30612930.268245130.27258100.9390.95599.98450.26
2.506-2.5940.29512360.248237920.251250320.9420.9699.9840.235
2.594-2.6910.27412670.231228940.233241650.9520.96799.98340.213
2.691-2.8010.28511480.227220750.23232240.9470.96799.99570.208
2.801-2.9260.26511580.217211370.219222970.9530.97199.9910.195
2.926-3.0690.26911020.213202360.216213400.9540.97299.99060.194
3.069-3.2350.2589940.217193190.219203140.9590.97299.99510.2
3.235-3.4310.2539740.22182650.222192390.9620.9741000.205
3.431-3.6680.2388300.203172710.205181010.9660.9781000.191
3.668-3.9610.2158220.178161120.18169340.9720.9831000.168
3.961-4.3390.1978040.151147420.154155470.9780.98799.99360.142
4.339-4.8510.1926680.144134730.147141410.9780.9881000.136
4.851-5.6010.1787080.146117910.148124990.9830.9891000.139
5.601-6.8580.1995460.155101090.157106550.9790.9881000.148
6.858-9.6930.1564130.13179090.13283220.9860.9911000.127
9.693-196.6620.2372240.20645660.20747970.9720.96199.85410.24

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