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- PDB-9i34: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in ... -

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Basic information

Entry
Database: PDB / ID: 9i34
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with hexanoyl-CoA
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer / hexanoyl-CoA / hexanol
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
HEXANOYL-COENZYME A / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)478,71424
Polymers468,32612
Non-polymers10,38812
Water40,2642235
1
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7864
Polymers78,0542
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-90 kcal/mol
Surface area23820 Å2
MethodPISA
2
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7864
Polymers78,0542
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-92 kcal/mol
Surface area23970 Å2
MethodPISA
3
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7864
Polymers78,0542
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15880 Å2
ΔGint-94 kcal/mol
Surface area23950 Å2
MethodPISA
4
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7864
Polymers78,0542
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-92 kcal/mol
Surface area23980 Å2
MethodPISA
5
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7864
Polymers78,0542
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-90 kcal/mol
Surface area24030 Å2
MethodPISA
6
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7864
Polymers78,0542
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15850 Å2
ΔGint-93 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.488, 276.488, 390.12
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-577-

HOH

21D-690-

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-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H46N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2235 / 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: 69.45 %
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: 1.95→225.58 Å / Num. obs: 538030 / % possible obs: 100 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.045 / Net I/σ(I): 12.6
Reflection shellResolution: 10.68→225.58 Å / Redundancy: 26 % / Rmerge(I) obs: 0.033 / Mean I/σ(I) obs: 61.5 / Num. unique obs: 3598 / CC1/2: 1 / Rpim(I) all: 0.006 / % 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: 1.95→225.579 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.087 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2333 27053 5.029 %
Rwork0.2046 510883 -
all0.206 --
obs-537936 99.981 %
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: 39.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.152 Å2-0 Å20 Å2
2--0.152 Å20 Å2
3----0.304 Å2
Refinement stepCycle: LAST / Resolution: 1.95→225.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32548 0 660 2235 35443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01234021
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631841
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.80846349
X-RAY DIFFRACTIONr_angle_other_deg0.6071.74773084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00354296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.7675336
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg5.5312.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.762105145
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.476101494
X-RAY DIFFRACTIONr_chiral_restr0.0860.25017
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0241505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027839
X-RAY DIFFRACTIONr_nbd_refined0.2250.27411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.230984
X-RAY DIFFRACTIONr_nbtor_refined0.1810.216763
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.217611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.22233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1270.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.218
X-RAY DIFFRACTIONr_nbd_other0.1770.2139
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.238
X-RAY DIFFRACTIONr_mcbond_it4.0363.75717211
X-RAY DIFFRACTIONr_mcbond_other4.0343.75717211
X-RAY DIFFRACTIONr_mcangle_it5.7266.73721489
X-RAY DIFFRACTIONr_mcangle_other5.7266.73721490
X-RAY DIFFRACTIONr_scbond_it4.424.01816810
X-RAY DIFFRACTIONr_scbond_other4.424.01816807
X-RAY DIFFRACTIONr_scangle_it6.4757.25724857
X-RAY DIFFRACTIONr_scangle_other6.4757.25724858
X-RAY DIFFRACTIONr_lrange_it8.14135.01838741
X-RAY DIFFRACTIONr_lrange_other8.12434.7738336
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
1.95-2.0010.33619780.326375970.326395890.9140.9299.96460.328
2.001-2.0550.32119790.305365180.306385040.9250.93399.98180.305
2.055-2.1150.32819310.302355520.304375010.9220.93399.9520.301
2.115-2.180.32218440.291345960.293364460.9310.94499.98350.283
2.18-2.2520.2917610.266335400.267353090.9440.95399.97730.253
2.252-2.3310.28217050.25324760.251341910.9480.9699.97070.232
2.331-2.4190.27617180.237313290.239330500.9510.96599.99090.216
2.419-2.5170.26916340.228301410.23317790.9550.96899.98740.205
2.517-2.6290.25815310.216290160.218305500.9590.97299.99020.193
2.629-2.7580.25714700.22276970.221291690.9580.97199.99310.195
2.758-2.9070.25813150.218264600.22277770.960.97299.99280.193
2.907-3.0830.23312400.211250600.212263010.9670.97499.99620.191
3.083-3.2960.25112530.221235200.223247780.9610.97199.97980.203
3.296-3.560.23111510.208218890.209230440.970.97799.98260.194
3.56-3.90.20410280.179202670.181212960.9770.98399.99530.168
3.9-4.360.17410160.151182820.152192980.9820.9871000.14
4.36-5.0340.1668640.139162490.14171130.9850.991000.129
5.034-6.1640.1857620.153137320.154144940.9830.9891000.144
6.164-8.7140.1725420.147108150.149113590.9850.98999.98240.14
8.714-225.5790.1733310.13961480.1464890.9830.9799.84590.133

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