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- PDB-6tzv: Crystal Structure of the carboxyltransferase subunit of ACC (AccD... -

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Basic information

Entry
Database: PDB / ID: 6tzv
TitleCrystal Structure of the carboxyltransferase subunit of ACC (AccD6) in complex with inhibitor Phenyl-Cyclodiaone from Mycobacterium tuberculosis
ComponentsProbable propionyl-CoA carboxylase beta chain 6
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE INHIBITOR ACCD6 / CARBOXYLTRANSFERASE BETA-SUBUNIT OF ACYL-COACARBOXYLASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / 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-PKP / 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: 2.388 Å
AuthorsReddy, M.C.M. / Zhou, N. / Sacchettini, J. / 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
CitationJournal: To Be Published
Title: Novel herbicidal derivatives that inhibit carboxyltransferase subunit of the acetyl-CoA carboxylase in Mycobacterium tuberculosis
Authors: Reddy, M.C.M. / Zhou, N. / Sacchettini, J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 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: Probable propionyl-CoA carboxylase beta chain 6
B: Probable propionyl-CoA carboxylase beta chain 6
C: Probable propionyl-CoA carboxylase beta chain 6
D: Probable propionyl-CoA carboxylase beta chain 6
E: Probable propionyl-CoA carboxylase beta chain 6
F: Probable propionyl-CoA carboxylase beta chain 6
G: Probable propionyl-CoA carboxylase beta chain 6
H: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,79116
Polymers401,5918
Non-polymers3,1998
Water20,3031127
1
A: Probable propionyl-CoA carboxylase beta chain 6
B: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1984
Polymers100,3982
Non-polymers8002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-45 kcal/mol
Surface area31480 Å2
MethodPISA
2
C: Probable propionyl-CoA carboxylase beta chain 6
D: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1984
Polymers100,3982
Non-polymers8002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-41 kcal/mol
Surface area30900 Å2
MethodPISA
3
E: Probable propionyl-CoA carboxylase beta chain 6
F: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1984
Polymers100,3982
Non-polymers8002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-42 kcal/mol
Surface area31600 Å2
MethodPISA
4
G: Probable propionyl-CoA carboxylase beta chain 6
H: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1984
Polymers100,3982
Non-polymers8002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-40 kcal/mol
Surface area31140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.345, 153.069, 150.184
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable propionyl-CoA carboxylase beta chain 6 / PCCase / Propanoyl-CoA:carbon dioxide ligase


Mass: 50198.934 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: accD6, Rv2247, MTCY427.28 / Plasmid: PET28b-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WQH5, propionyl-CoA carboxylase
#2: Chemical
ChemComp-PKP / 4'-[(6-chloro-1,3-benzothiazol-2-yl)oxy]-6-hydroxy-4,4-dimethyl-4,5-dihydro[1,1'-biphenyl]-2(3H)-one


Mass: 399.891 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H18ClNO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1127 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Li2SO4, 0.1 M Tris pH 7, 1 M potassium sodium tartarate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0,987
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
29871
ReflectionResolution: 2.388→35.76 Å / Num. obs: 180446 / % possible obs: 98.69 % / Redundancy: 1.36 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Net I/σ(I): 32.5
Reflection shellResolution: 2.43→2.48 Å / Num. unique obs: 2463 / CC1/2: 0.89 / % possible all: 98.2

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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: 2.388→35.76 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 9047 5.01 %
Rwork0.1664 171399 -
obs0.1683 180446 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 41.0472 Å2 / Biso min: 18.68 Å2
Refinement stepCycle: final / Resolution: 2.388→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24639 0 216 1127 25982
Biso mean--40.58 42.4 -
Num. residues----3375
LS refinement shell

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

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3885-2.41560.26652670.2041486585
2.4156-2.4440.24752960.1849578699
2.444-2.47380.24723000.1823568399
2.4738-2.50520.21983060.1794577399
2.5052-2.53810.23573040.1771571799
2.5381-2.57290.2393110.1851571299
2.5729-2.60960.24363490.1885569699
2.6096-2.64860.26123030.1875574399
2.6486-2.68990.23463120.1807575099
2.6899-2.7340.24142970.1728575899
2.734-2.78110.23232910.183572899
2.7811-2.83170.24392810.183569598
2.8317-2.88610.24243180.18855714100
2.8861-2.9450.23582820.18635780100
2.945-3.0090.24523180.18765734100
3.009-3.0790.21982890.18275794100
3.079-3.15590.223080.18345712100
3.1559-3.24120.22982800.1875577599
3.2412-3.33650.21853070.18025770100
3.3365-3.44410.22513240.1759565498
3.4441-3.56710.19362660.1639576399
3.5671-3.70980.19343030.16175796100
3.7098-3.87840.19543030.16025743100
3.8784-4.08270.17412930.15335801100
4.0827-4.3380.18523010.1485577599
4.338-4.67230.16482930.1324569098
4.6723-5.14130.16683400.1445759100
5.1413-5.88240.19523250.17055776100
5.8824-7.40040.22662930.1705578798
7.40040.15472870.1479567096

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