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- PDB-9i2t: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 9i2t
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homodimer
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
ACETATE ION / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMojanaga, O.O. / Acharya, K.R. / Lloyd, M.D.
Funding support1items
OrganizationGrant numberCountry
Other government
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)468,97523
Polymers468,32612
Non-polymers64911
Water14,232790
1
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2315
Polymers78,0542
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-81 kcal/mol
Surface area24900 Å2
MethodPISA
2
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1133
Polymers78,0542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-79 kcal/mol
Surface area24930 Å2
MethodPISA
3
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1133
Polymers78,0542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-78 kcal/mol
Surface area24800 Å2
MethodPISA
4
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1133
Polymers78,0542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-80 kcal/mol
Surface area25280 Å2
MethodPISA
5
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2315
Polymers78,0542
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-82 kcal/mol
Surface area24830 Å2
MethodPISA
6
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1724
Polymers78,0542
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-83 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)275.45, 275.45, 388.331
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.98 Å3/Da / Density % sol: 69.14 %
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: Sep 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 2.4→224.67 Å / Num. obs: 286594 / % possible obs: 100 % / Redundancy: 27.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.404 / Rpim(I) all: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 13.15→224.67 Å / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 23.6 / Num. unique obs: 1959 / CC1/2: 0.999 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / % 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: 2.4→224.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.376 / SU ML: 0.198 / Cross valid method: FREE R-VALUE / ESU R: 0.251 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2504 14384 5.019 %
Rwork0.2118 272194 -
all0.214 --
obs-286578 99.994 %
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: 61.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20 Å2
2--0.1 Å20 Å2
3----0.199 Å2
Refinement stepCycle: LAST / Resolution: 2.4→224.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32200 0 44 790 33034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01232989
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631017
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.79844846
X-RAY DIFFRACTIONr_angle_other_deg0.5561.74871155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47854229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.8715312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.613105084
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.21101480
X-RAY DIFFRACTIONr_chiral_restr0.0740.24840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0240595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027697
X-RAY DIFFRACTIONr_nbd_refined0.2360.27605
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.230474
X-RAY DIFFRACTIONr_nbtor_refined0.1810.216035
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.217303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.21389
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.22
X-RAY DIFFRACTIONr_nbd_other0.1190.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.060.29
X-RAY DIFFRACTIONr_mcbond_it6.1536.0516999
X-RAY DIFFRACTIONr_mcbond_other6.156.0516998
X-RAY DIFFRACTIONr_mcangle_it9.42910.84221193
X-RAY DIFFRACTIONr_mcangle_other9.4310.84221194
X-RAY DIFFRACTIONr_scbond_it5.246.30815990
X-RAY DIFFRACTIONr_scbond_other5.2386.30715987
X-RAY DIFFRACTIONr_scangle_it8.15211.46123653
X-RAY DIFFRACTIONr_scangle_other8.14911.46123651
X-RAY DIFFRACTIONr_lrange_it11.68453.78837092
X-RAY DIFFRACTIONr_lrange_other11.69353.78137012
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
2.4-2.4620.35210430.353199910.353210360.9060.90499.99050.356
2.462-2.530.34110910.338194200.338205130.9160.91799.99020.34
2.53-2.6030.3359280.31190170.311199470.9220.93399.990.311
2.603-2.6830.3329400.297184280.299193700.9310.94299.98970.294
2.683-2.7710.3199480.288178660.29188140.9330.9451000.283
2.771-2.8680.3218960.27173320.272182290.9360.95499.99450.259
2.868-2.9770.39810.243165160.246174980.9420.96299.99430.228
2.977-3.0980.2818130.235161390.237169550.9510.96599.98230.217
3.098-3.2360.2798480.231154060.233162540.9470.9671000.213
3.236-3.3940.2737550.226147610.228155160.9530.9711000.211
3.394-3.5770.2637260.218140920.22148190.960.97599.99330.205
3.577-3.7940.2327210.203132690.204139900.9680.9791000.192
3.794-4.0560.2196150.188125920.19132070.9730.9821000.181
4.056-4.3810.2035990.171116970.173122960.9760.9831000.166
4.381-4.7990.2125530.169107730.171113270.9730.98399.99120.167
4.799-5.3650.2125330.16497780.166103110.9760.9861000.165
5.365-6.1950.2394400.17686920.17991320.970.9841000.176
6.195-7.5860.2264020.17673690.17977710.9720.9841000.181
7.586-10.7220.1563190.12257680.12460870.9870.9921000.136
10.722-224.670.2312330.2332880.2335240.9670.95299.91490.268

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