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

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Basic information

Entry
Database: PDB / ID: 6prw
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 / Center for Structural Genomics of Infectious Diseases / CSGID / TB Structural Genomics Consortium / TBSGC / PSI-2 / Protein Structure Initiative
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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Chem-OWD / 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: 2.609 Å
AuthorsReddy, M.C.M. / Nian, Z. / Michele, S.T.C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD) United States
Citation
Journal: To Be Published
Title: CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD6) IN COMPLEX WITH INHIBITOR QUIZALOFOP-P DEVERIVATIVE FROM MYCOBACTERIUM TUBERCULOSIS
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
DepositionJul 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 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)404,10916
Polymers401,5918
Non-polymers2,5188
Water9,620534
1
A: Propionyl-CoA carboxylase subunit beta
B: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0274
Polymers100,3982
Non-polymers6292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-43 kcal/mol
Surface area31710 Å2
MethodPISA
2
C: Propionyl-CoA carboxylase subunit beta
D: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0274
Polymers100,3982
Non-polymers6292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-38 kcal/mol
Surface area31110 Å2
MethodPISA
3
E: Propionyl-CoA carboxylase subunit beta
F: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0274
Polymers100,3982
Non-polymers6292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-42 kcal/mol
Surface area31980 Å2
MethodPISA
4
G: Propionyl-CoA carboxylase subunit beta
H: Propionyl-CoA carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0274
Polymers100,3982
Non-polymers6292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-39 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.782, 150.406, 152.644
Angle α, β, γ (deg.)90.000, 89.730, 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
Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E7XNZ4, UniProt: P9WQH5*PLUS, propionyl-CoA carboxylase
#2: Chemical
ChemComp-OWD / {4-[(6-chloroquinoxalin-2-yl)oxy]phenyl}acetic acid


Mass: 314.723 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1000 mM Potassium sodium tartrate 100 mM Tris base/ Hydrochloric acid pH 7.0 200 mM Lithium sulfate
PH range: 7.5-8.0

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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: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→42.536 Å / Num. obs: 133806 / % possible obs: 94.96 % / Redundancy: 6 % / Net I/σ(I): 1.33
Reflection shellResolution: 2.6→2.8 Å / Num. unique obs: 2770

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.609→42.536 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.2386 6712 5.02 %
Rwork0.1846 --
obs0.1873 133806 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.4 Å2 / Biso mean: 45.4501 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: final / Resolution: 2.609→42.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24644 0 176 534 25354
Biso mean--41.81 42.47 -
Num. residues----3376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.609-2.630.18162530.1598450799
2.6092-2.63890.32291470.2865277061
2.6389-2.66990.3712270.2854394190
2.6699-2.70250.36262320.2919407891
2.7025-2.73670.34822190.2938407292
2.7367-2.77270.37892200.3012407392
2.7727-2.81070.36952350.2874405093
2.8107-2.85080.38042170.2902414792
2.8508-2.89330.35252010.2916418894
2.8933-2.93850.3282090.2761423494
2.9385-2.98670.35682190.2709415294
2.9867-3.03820.31951950.2552425995
3.0382-3.09340.34262050.2444423895
3.0934-3.15290.28282120.2342428296
3.1529-3.21720.29412070.2212431196
3.2172-3.28720.25032490.2142427196
3.2872-3.36360.28392130.2116430497
3.3636-3.44770.26882490.1917432697
3.4477-3.54090.28672150.1845434597
3.5409-3.6450.22142310.1706434998
3.645-3.76260.22242450.1607433298
3.7626-3.8970.19772400.155437198
3.897-4.05290.22042390.1427440199
4.0529-4.23720.19022280.1391443999
4.2372-4.46040.17232500.1267441499
4.4604-4.73950.1662200.1157442399
4.7395-5.10490.16882300.1331445199
5.1049-5.61750.19632440.1547441599
5.6175-6.4280.24272170.1736449299
6.428-8.08950.17862440.1596445999

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