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- PDB-8rp5: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (E2... -

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Basic information

Entry
Database: PDB / ID: 8rp5
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (E241A mutant)
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 / 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
TRIETHYLENE GLYCOL / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 12, 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

Downloads & links

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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)78,7239
Polymers78,2012
Non-polymers5237
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-62 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.619, 78.989, 58.923
Angle α, β, γ (deg.)90.000, 92.191, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-methylacyl-CoA racemase / AMACR / MtMCR


Mass: 39100.289 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.71437407 Å3/Da / Density % sol: 54.71 %
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, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.85→90.244 Å / Num. obs: 70688 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.081 / Rrim(I) all: 0.152 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.06-90.246.70.02543180.9990.0150.029
1.85-1.896.91.823300790.51.1422.156

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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: 1.85→90.244 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.175 / SU B: 4.591 / SU ML: 0.126 / Average fsc free: 0.9477 / Average fsc work: 0.9611 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2363 3590 5.08 %
Rwork0.193 67077 -
all0.195 --
obs-70667 99.967 %
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: 31.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.083 Å2-0 Å20.418 Å2
2---2.186 Å20 Å2
3---2.065 Å2
Refinement stepCycle: LAST / Resolution: 1.85→90.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 34 414 5806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0125520
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165217
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.8087492
X-RAY DIFFRACTIONr_angle_other_deg0.8031.74711969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.764552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77910847
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.03410247
X-RAY DIFFRACTIONr_chiral_restr0.1180.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
X-RAY DIFFRACTIONr_nbd_refined0.2440.21232
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.25136
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22737
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.22926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2361
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1320.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.218
X-RAY DIFFRACTIONr_nbd_other0.2610.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.223
X-RAY DIFFRACTIONr_mcbond_it4.1523.182828
X-RAY DIFFRACTIONr_mcbond_other4.1523.182828
X-RAY DIFFRACTIONr_mcangle_it5.3855.6963528
X-RAY DIFFRACTIONr_mcangle_other5.3855.6983529
X-RAY DIFFRACTIONr_scbond_it5.0123.4672692
X-RAY DIFFRACTIONr_scbond_other5.0113.4672693
X-RAY DIFFRACTIONr_scangle_it6.866.2143964
X-RAY DIFFRACTIONr_scangle_other6.8596.2133965
X-RAY DIFFRACTIONr_lrange_it8.01332.6686338
X-RAY DIFFRACTIONr_lrange_other7.99431.856252
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
1.85-1.8980.3412420.33449740.33552200.8940.89299.92340.339
1.898-1.950.3322470.30947630.3150120.9140.92699.96010.31
1.95-2.0070.3262290.28447150.28649450.920.93899.97980.282
2.007-2.0680.2742500.25745590.25848110.9490.95199.95840.252
2.068-2.1360.2912510.24444100.24646630.9390.95699.95710.234
2.136-2.2110.2932350.22742300.2344690.9420.96499.91050.214
2.211-2.2940.2842180.25241320.25343520.9130.95199.9540.233
2.294-2.3880.2642040.20239670.20541710.9560.9741000.182
2.388-2.4940.2791940.19238110.19640060.9550.97799.9750.172
2.494-2.6160.2321980.1836260.18338260.9640.9899.94770.16
2.616-2.7570.2281930.18134780.18436710.9640.9811000.159
2.757-2.9240.2471820.17632720.17934550.9640.98199.97110.157
2.924-3.1260.2141750.1630690.16232440.9720.9841000.147
3.126-3.3760.2321610.17228680.17430300.9690.98399.9670.159
3.376-3.6980.2211480.17826530.1828010.9710.9831000.169
3.698-4.1330.1951220.16524160.16625380.9790.9841000.161
4.133-4.7710.1831160.14421090.14622250.980.9881000.144
4.771-5.8390.1711060.15418200.15519260.9830.9891000.156
5.839-8.2410.246680.17214100.17514780.9710.9851000.174
8.241-90.2440.183510.1787950.1788470.9780.97299.88190.186

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