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- PDB-9i30: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in ... -

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Basic information

Entry
Database: PDB / ID: 9i30
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with ketoprofenoyl-CoA
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer / ketoprofenoyl-CoA / ketoprofen
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
: / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)480,37124
Polymers468,32612
Non-polymers12,04612
Water27,1131505
1
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0624
Polymers78,0542
Non-polymers2,0082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-77 kcal/mol
Surface area23470 Å2
MethodPISA
2
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0624
Polymers78,0542
Non-polymers2,0082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16060 Å2
ΔGint-78 kcal/mol
Surface area23800 Å2
MethodPISA
3
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0624
Polymers78,0542
Non-polymers2,0082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-78 kcal/mol
Surface area23700 Å2
MethodPISA
4
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0624
Polymers78,0542
Non-polymers2,0082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-79 kcal/mol
Surface area23850 Å2
MethodPISA
5
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0624
Polymers78,0542
Non-polymers2,0082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16080 Å2
ΔGint-77 kcal/mol
Surface area23840 Å2
MethodPISA
6
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0624
Polymers78,0542
Non-polymers2,0082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-75 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.694, 276.694, 390.43
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-542-

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-A1IZD / (S)-ketoprofenoyl-CoA / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (2~{S})-2-[3-(phenylcarbonyl)phenyl]propanethioate


Mass: 1003.799 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C37H48N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1505 / 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: 4.02 Å3/Da / Density % sol: 69.41 %
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: 2.08→225.751 Å / Num. obs: 444942 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.302 / Rpim(I) all: 0.059 / Net I/σ(I): 7.9
Reflection shellResolution: 11.39→225.75 Å / Redundancy: 25.6 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 2996 / CC1/2: 0.992 / Rpim(I) all: 0.016 / % possible all: 99.9

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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: 2.08→225.751 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.977 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.16 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2507 22435 5.043 %
Rwork0.2161 422418 -
all0.218 --
obs-444853 99.979 %
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: 46.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.174 Å20 Å2-0 Å2
2---0.174 Å2-0 Å2
3---0.349 Å2
Refinement stepCycle: LAST / Resolution: 2.08→225.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32322 0 792 1505 34619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01233926
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631663
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.8146229
X-RAY DIFFRACTIONr_angle_other_deg0.5841.74772623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1954250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.4876.875384
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.93612.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67105109
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.428101480
X-RAY DIFFRACTIONr_chiral_restr0.080.24987
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0241370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027898
X-RAY DIFFRACTIONr_nbd_refined0.230.27615
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.231232
X-RAY DIFFRACTIONr_nbtor_refined0.1840.216660
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.217615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.21879
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.28
X-RAY DIFFRACTIONr_nbd_other0.1460.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.217
X-RAY DIFFRACTIONr_mcbond_it4.4094.54817066
X-RAY DIFFRACTIONr_mcbond_other4.4094.54817066
X-RAY DIFFRACTIONr_mcangle_it6.5468.15321294
X-RAY DIFFRACTIONr_mcangle_other6.5468.15321295
X-RAY DIFFRACTIONr_scbond_it4.414.83616860
X-RAY DIFFRACTIONr_scbond_other4.414.83616861
X-RAY DIFFRACTIONr_scangle_it6.6428.76724935
X-RAY DIFFRACTIONr_scangle_other6.6428.76724936
X-RAY DIFFRACTIONr_lrange_it8.76541.57538585
X-RAY DIFFRACTIONr_lrange_other8.76941.58638333
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
2.08-2.1340.35315820.348310780.348326630.9020.90599.99080.351
2.134-2.1930.33815010.334303780.334318800.9150.91799.99690.338
2.193-2.2560.32815400.311294470.312309890.9250.93299.99350.314
2.256-2.3250.31414110.291287620.292301740.9350.94499.99670.29
2.325-2.4020.30414880.273276650.275291570.940.95299.98630.267
2.402-2.4860.30814370.265268660.267283070.9420.95899.98590.254
2.486-2.580.30813920.257258530.26272500.940.95999.98170.244
2.58-2.6850.29413020.24250090.242263180.9480.96699.97340.221
2.685-2.8050.31413440.25238620.253252110.930.96399.98020.229
2.805-2.9410.2911520.241230110.243241670.9490.96699.98340.221
2.941-3.1010.28412770.239216650.241229460.950.96899.98260.223
3.101-3.2890.28710550.25207190.251217780.9520.96799.98160.236
3.289-3.5160.27110860.24193830.242204750.9630.97399.97070.231
3.516-3.7970.24610140.207180540.209190800.9670.9899.93710.2
3.797-4.1590.2149540.177166560.179176190.9740.98399.94890.174
4.159-4.650.1718210.146151420.147159670.9820.98899.97490.147
4.65-5.3690.1846830.143134400.145141280.9830.98999.96460.147
5.369-6.5750.1876320.15114050.152120400.9830.9999.97510.153
6.575-9.2950.1794570.14289340.14493930.9840.99199.97870.148
9.295-225.7510.1673070.1750890.1754050.9820.95699.83350.208

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