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- PDB-8rmw: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis. -

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Basic information

Entry
Database: PDB / ID: 8rmw
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis.
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer
Function / homology
Function and homology information


alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / formyl-CoA transferase / formyl-CoA transferase activity / organic substance metabolic process
Similarity search - Function
CoA-transferase family III domain 3 superfamily / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMojanaga, O.O. / Acharya, K.R. / Lloyd, M.D.
Funding supportBotswana, 1items
OrganizationGrant numberCountry
Other governmentBotswana
CitationJournal: Biomolecules / Year: 2024
Title: alpha-Methylacyl-CoA Racemase from Mycobacterium tuberculosis -Detailed Kinetic and Structural Characterization of the Active Site.
Authors: Mojanaga, O.O. / Woodman, T.J. / Lloyd, M.D. / Acharya, K.R.
History
DepositionJan 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6096
Polymers78,3172
Non-polymers2924
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.053, 79.090, 59.194
Angle α, β, γ (deg.)90.000, 92.008, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-methylacyl-CoA racemase / / CoA transferase / Fatty acid-CoA racemase


Mass: 39158.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: frc_2, frc, frc_3, mcr, DSI46_17980, ERS007679_00285, ERS007681_01258, ERS007720_00852, ERS007722_01391, ERS053720_03198, F6W99_03855, GJE03_06060, SAMEA2683035_02587
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A045IZ15, formyl-CoA transferase, alpha-methylacyl-CoA racemase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74398351 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 0.1 M sodium (HEPES-MOPS)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→90.471 Å / Num. obs: 100251 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.057 / Rrim(I) all: 0.108 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.04-90.476.60.0265410.0120.023
1.65-1.686.92.39849080.321.4882.828

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→90.471 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.177 / SU B: 3.133 / SU ML: 0.095 / Average fsc free: 0.9452 / Average fsc work: 0.9557 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2251 5092 5.079 %
Rwork0.1944 95155 -
all0.196 --
obs-100247 99.996 %
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: 30.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.349 Å2-0 Å20.299 Å2
2---0.99 Å2-0 Å2
3---1.315 Å2
Refinement stepCycle: LAST / Resolution: 1.65→90.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 19 421 5806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125527
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165203
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.8097513
X-RAY DIFFRACTIONr_angle_other_deg0.5851.74811946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.697552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04410853
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.58110250
X-RAY DIFFRACTIONr_chiral_restr0.0870.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021283
X-RAY DIFFRACTIONr_nbd_refined0.2210.21091
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24785
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22733
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2357
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.26
X-RAY DIFFRACTIONr_nbd_other0.2280.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.220
X-RAY DIFFRACTIONr_mcbond_it2.7813.1342836
X-RAY DIFFRACTIONr_mcbond_other2.7813.1342836
X-RAY DIFFRACTIONr_mcangle_it3.8275.6233540
X-RAY DIFFRACTIONr_mcangle_other3.8275.6243541
X-RAY DIFFRACTIONr_scbond_it3.5673.4472691
X-RAY DIFFRACTIONr_scbond_other3.5673.4472692
X-RAY DIFFRACTIONr_scangle_it5.3796.1883971
X-RAY DIFFRACTIONr_scangle_other5.3796.1883972
X-RAY DIFFRACTIONr_lrange_it6.45630.7126219
X-RAY DIFFRACTIONr_lrange_other6.44729.5986129
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
1.65-1.6930.3913850.36669780.36773630.8730.8941000.37
1.693-1.7390.3383750.34368240.34371990.9090.9051000.349
1.739-1.790.3293310.32166530.32169840.9080.9181000.326
1.79-1.8450.3143550.28964220.2967770.9270.9381000.292
1.845-1.9050.2963430.27762830.27866270.9390.94699.98490.277
1.905-1.9720.2873440.25960320.2663770.9390.95399.98430.253
1.972-2.0460.2753150.23658520.23861670.9480.9631000.228
2.046-2.130.2742700.22156380.22359080.9540.9681000.211
2.13-2.2250.2343050.253850.20256900.9640.9751000.189
2.225-2.3330.2352590.19651900.19854510.9660.97799.96330.183
2.333-2.4590.2262620.18649280.18851900.9670.9791000.174
2.459-2.6080.222380.18546530.18748910.9710.981000.174
2.608-2.7880.2322120.18744030.18946150.9670.9791000.175
2.788-3.0110.2442240.18840790.19143030.9630.9791000.179
3.011-3.2980.2242040.17637710.17839750.9690.9821000.169
3.298-3.6870.22020.17833660.17935680.9810.9841000.172
3.687-4.2560.1931720.15130050.15431770.9760.9871000.143
4.256-5.210.1461190.1325820.1327010.9890.9921000.12
5.21-7.3560.1761270.17519650.17520920.9840.9881000.168
7.356-90.4710.184500.17411460.17511960.9810.9781000.162

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