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- PDB-6pk2: CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD... -

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Basic information

Entry
Database: PDB / ID: 6pk2
TitleCRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD6) IN COMPLEX WITH INHIBITOR QUIZALOFOP-P derivative FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsPropionyl-CoA carboxylase subunit beta
KeywordsTRANSFERASE / CROTONASE SUPER FAMILY / CARBOXYLTRANSFERASE / TRANSFERASE-HERBICIDE / Structural Genomics / PSI-Biology / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / fatty acid elongation, saturated fatty acid / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / peptidoglycan-based cell wall / transferase activity
Similarity search - Function
Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-ORJ / Propionyl-CoA carboxylase subunit beta / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta6 subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.402 Å
AuthorsReddy, M.C.M. / Nian, Z. / Michele, T.C.B. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
Citation
Journal: To Be Published
Title: Elucidating the Inhibition and specificity of binding of herbicidal aryloxyphenoxypropionates derivatives to Mycobacterium tuberculosis carboxyltransferase domain of acetyl-coenzyme A(AccD6).
Authors: Reddy, M.C.M. / Nian, Z. / Sacchettini, J.C.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2014
Title: Structure, Activity, and Inhibition of the Carboxyltransferase beta-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis
Authors: Reddy, M.C.M. / Sacchettini, J.C.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Propionyl-CoA carboxylase subunit beta
B: Propionyl-CoA carboxylase subunit beta
C: Propionyl-CoA carboxylase subunit beta
D: Propionyl-CoA carboxylase subunit beta
E: Propionyl-CoA carboxylase subunit beta
F: Propionyl-CoA carboxylase subunit beta
G: Propionyl-CoA carboxylase subunit beta
H: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,25016
Polymers401,5918
Non-polymers2,6598
Water18,6091033
1
A: Propionyl-CoA carboxylase subunit beta
B: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0634
Polymers100,3982
Non-polymers6652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-41 kcal/mol
Surface area31690 Å2
MethodPISA
2
C: Propionyl-CoA carboxylase subunit beta
D: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0634
Polymers100,3982
Non-polymers6652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-39 kcal/mol
Surface area31190 Å2
MethodPISA
3
E: Propionyl-CoA carboxylase subunit beta
F: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0634
Polymers100,3982
Non-polymers6652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-41 kcal/mol
Surface area31700 Å2
MethodPISA
4
G: Propionyl-CoA carboxylase subunit beta
H: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0634
Polymers100,3982
Non-polymers6652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-36 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.120, 149.797, 152.958
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Propionyl-CoA carboxylase subunit beta / / Propionyl-CoA carboxylase subunit beta 6


Mass: 50198.934 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: accD6, DSI35_30190, ERS023446_01401, ERS024213_00063, ERS027644_00734, ERS027646_00895, ERS027651_00104, ERS027653_02606, ERS027656_00219, ERS027666_02199, ERS031537_00601, ERS124361_03148, ...Gene: accD6, DSI35_30190, ERS023446_01401, ERS024213_00063, ERS027644_00734, ERS027646_00895, ERS027651_00104, ERS027653_02606, ERS027656_00219, ERS027666_02199, ERS031537_00601, ERS124361_03148, SAMEA2682864_00423, SAMEA2683035_01247
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E7XNZ4, UniProt: P9WQH5*PLUS, propionyl-CoA carboxylase
#2: Chemical
ChemComp-ORJ / 2-{4-[(6-fluoro-1,3-benzothiazol-2-yl)oxy]-2-hydroxyphenyl}-N-methylacetamide


Mass: 332.349 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H13FN2O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1033 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1M potassium sodium tartrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 25, 2016 / Details: NULL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→48.444 Å / Num. obs: 176652 / % possible obs: 98.73 % / Redundancy: 1.35 % / Net I/σ(I): 1.35
Reflection shellResolution: 2.4→5.7 Å / Num. unique obs: 12677

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→48.444 Å / FOM work R set: 0.8547 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 2017 1.14 %
Rwork0.173 174635 -
obs0.1735 176652 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.17 Å2 / Biso mean: 43.59 Å2 / Biso min: 19.85 Å2
Refinement stepCycle: final / Resolution: 2.402→48.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24651 0 184 1033 25868
Biso mean--37.98 44.18 -
Num. residues----3376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825376
X-RAY DIFFRACTIONf_angle_d1.08134552
X-RAY DIFFRACTIONf_chiral_restr0.0743948
X-RAY DIFFRACTIONf_plane_restr0.0054576
X-RAY DIFFRACTIONf_dihedral_angle_d14.2488912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4022-2.46220.25891380.2203117001183893
2.4622-2.52880.26761480.2094124281257699
2.5288-2.60320.24451430.1996123751251899
2.6032-2.68720.2581480.1965125211266999
2.6872-2.78330.24741360.193124571259399
2.7833-2.89470.25621550.1931124461260199
2.8947-3.02640.23541330.1977124861261999
3.0264-3.1860.27741530.1985125601271399
3.186-3.38550.2631490.1911253512684100
3.3855-3.64680.21531350.1683125971273299
3.6468-4.01370.19931490.15991258712736100
4.0137-4.59410.17681430.14271257712720100
4.5941-5.78650.22951430.15931268912832100
5.7865-48.45370.1811440.1586126771282199

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