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- PDB-8rp3: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (H1... -

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Basic information

Entry
Database: PDB / ID: 8rp3
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (H126A 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 / bile acid metabolic process / protein homodimerization activity
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
Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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

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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)78,3695
Polymers78,1832
Non-polymers1863
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-67 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.106, 79.153, 59.103
Angle α, β, γ (deg.)90, 91.656, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 359 / Label seq-ID: 2 - 360

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 39091.254 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.73654652 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging 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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.45→90.52 Å / Num. obs: 30851 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.982 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.228 / Rrim(I) all: 0.434 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.83-90.526.80.0556970.9970.0330.064
2.45-2.556.13.09334540.2782.0663.731

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→90.515 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.885 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.172 / SU B: 13.372 / SU ML: 0.272 / Average fsc free: 0.9382 / Average fsc work: 0.962 / Cross valid method: FREE R-VALUE / ESU R: 0.395 / ESU R Free: 0.281
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2618 1468 4.759 %
Rwork0.1875 29379 -
all0.191 --
obs-30847 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: 48.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.136 Å20 Å20.69 Å2
2---2.912 Å2-0 Å2
3---2.732 Å2
Refinement stepCycle: LAST / Resolution: 2.45→90.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 12 61 5429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0125502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165201
X-RAY DIFFRACTIONr_angle_refined_deg2.6451.8087478
X-RAY DIFFRACTIONr_angle_other_deg0.851.74811932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9555704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.575552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32510850
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.10710248
X-RAY DIFFRACTIONr_chiral_restr0.1140.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
X-RAY DIFFRACTIONr_nbd_refined0.2390.21233
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.25086
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22694
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.23015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2154
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.27
X-RAY DIFFRACTIONr_nbd_other0.270.230
X-RAY DIFFRACTIONr_mcbond_it7.0064.6842828
X-RAY DIFFRACTIONr_mcbond_other6.9944.6852828
X-RAY DIFFRACTIONr_mcangle_it9.5158.3963528
X-RAY DIFFRACTIONr_mcangle_other9.5168.3983529
X-RAY DIFFRACTIONr_scbond_it7.8284.9452674
X-RAY DIFFRACTIONr_scbond_other7.8264.9452675
X-RAY DIFFRACTIONr_scangle_it10.2448.9263950
X-RAY DIFFRACTIONr_scangle_other10.2428.9263951
X-RAY DIFFRACTIONr_lrange_it11.58541.8886082
X-RAY DIFFRACTIONr_lrange_other11.58641.8876083
X-RAY DIFFRACTIONr_ncsr_local_group_10.1140.0510634
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.11350.05008
12AX-RAY DIFFRACTIONLocal ncs0.11350.05008
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
2.45-2.5140.3831000.34721450.34922460.8690.88699.95550.349
2.514-2.5820.3021010.31521110.31422140.9160.91799.90970.317
2.582-2.6570.342990.28720550.2921540.910.9421000.29
2.657-2.7390.3071090.26720030.26921120.9310.9511000.266
2.739-2.8290.356700.25319690.25720390.9140.9551000.25
2.829-2.9280.312870.22918420.23319290.9260.9641000.224
2.928-3.0380.307870.21917960.22318830.9270.9671000.211
3.038-3.1620.33810.20717600.21218410.9330.9711000.195
3.162-3.3030.291020.21816490.22217510.9440.9691000.205
3.303-3.4640.263770.18715940.19116710.9520.9791000.175
3.464-3.6510.238820.17515080.17815900.9620.9841000.163
3.651-3.8720.26650.1614160.16414810.9560.9871000.151
3.872-4.1380.2640.14313690.14614330.9740.9881000.133
4.138-4.4690.226750.12712610.13113370.9690.99199.92520.119
4.469-4.8950.225660.11911510.12412170.970.9931000.113
4.895-5.470.173620.1110470.11311100.9840.99599.90990.105
5.47-6.3130.222480.1539220.1569700.9690.9891000.144
6.313-7.7220.236420.1517950.1568370.9630.9861000.145
7.722-10.8810.177320.1246240.1266560.9790.9911000.123
10.881-90.5150.397190.2883620.2933820.8720.94599.73820.292

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