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- PDB-4g2r: Crystal Structure of the carboxyltransferase subunit of ACC (AccD... -

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Basic information

Entry
Database: PDB / ID: 4g2r
TitleCrystal Structure of the carboxyltransferase subunit of ACC (AccD6) in complex with inhibitor haloxyfop from Mycobacterium tuberculosis
ComponentsAccD6, Carboxyltransferase beta-subunit of Acyl-CoA Carboxylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / TB Structural Genomics Consortium / TBSGC / crotonase super family / Carboxyltransferase / Transferase-herbicide complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / fatty acid elongation, saturated fatty acid / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / ligase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / 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-H1L / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta6 subunit / 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: 2.28 Å
AuthorsReddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sherekar, M. / Valluru, S. / Ehrenfeld, H. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: 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. / Breda, A. / Bruning, J.B. / Sherekar, M. / Valluru, S. / Thurman, C. / Ehrenfeld, H. / Sacchettini, J.C.
History
DepositionJul 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AccD6, Carboxyltransferase beta-subunit of Acyl-CoA Carboxylase
B: AccD6, Carboxyltransferase beta-subunit of Acyl-CoA Carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8456
Polymers100,3982
Non-polymers1,4474
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-38 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.780, 126.240, 161.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein AccD6, Carboxyltransferase beta-subunit of Acyl-CoA Carboxylase / PCCase / Propanoyl-CoA:carbon dioxide ligase


Mass: 50198.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: accD6, MT2307, MTCY427.28, Rv2247 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63407, UniProt: P9WQH5*PLUS, propionyl-CoA carboxylase
#2: Chemical
ChemComp-H1L / (2R)-2-(4-{[3-chloro-5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoic acid / HALOXYFOP INHIBITOR, R enantiomer


Mass: 361.700 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H11ClF3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 3.5 M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) LIQUID N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7 % / Av σ(I) over netI: 7.2 / Number: 384878 / Rsym value: 0.078 / D res high: 2.283 Å / D res low: 58.944 Å / Num. obs: 54953 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.2258.9499.910.040.047
5.17.2210010.0590.0596.5
4.175.110010.0530.0536.9
3.614.1710010.0580.0587
3.233.6110010.0720.0727.1
2.953.2310010.0950.0957.2
2.732.9510010.1430.1437.2
2.552.7310010.2370.2377.3
2.412.5510010.350.357.3
2.282.4199.910.5080.5086.3
ReflectionResolution: 2.28→58.944 Å / Num. obs: 54953 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.9
Reflection shellResolution: 2.28→2.41 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.508 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FB8

4fb8


Resolution: 2.28→58.94 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.33 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.198 1996 3.63 %
Rwork0.164 --
obs0.165 54917 99.9 %
all-54917 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.81 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7144 Å20 Å2-0 Å2
2--7.2796 Å2-0 Å2
3----11.994 Å2
Refinement stepCycle: LAST / Resolution: 2.28→58.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6467 0 96 691 7254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096777
X-RAY DIFFRACTIONf_angle_d1.139235
X-RAY DIFFRACTIONf_dihedral_angle_d14.5782441
X-RAY DIFFRACTIONf_chiral_restr0.0831042
X-RAY DIFFRACTIONf_plane_restr0.0051219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.283-2.34010.32171470.26633709X-RAY DIFFRACTION100
2.3401-2.40340.33821450.25443759X-RAY DIFFRACTION100
2.4034-2.47410.2721360.22683732X-RAY DIFFRACTION100
2.4741-2.5540.28061320.19983747X-RAY DIFFRACTION100
2.554-2.64520.25571380.19783744X-RAY DIFFRACTION100
2.6452-2.75120.2381430.18773768X-RAY DIFFRACTION100
2.7512-2.87640.25441380.18633763X-RAY DIFFRACTION100
2.8764-3.0280.2391480.18333751X-RAY DIFFRACTION100
3.028-3.21770.20261360.17363765X-RAY DIFFRACTION100
3.2177-3.46610.21450.15773793X-RAY DIFFRACTION100
3.4661-3.81490.1651470.14583782X-RAY DIFFRACTION100
3.8149-4.36670.17361350.1293818X-RAY DIFFRACTION100
4.3667-5.5010.13841450.12143821X-RAY DIFFRACTION100
5.501-58.96380.17111610.1683969X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -37.0146 Å / Origin y: -22.9992 Å / Origin z: 40.3613 Å
111213212223313233
T0.1755 Å2-0.0144 Å2-0.009 Å2-0.173 Å2-0.0368 Å2--0.2275 Å2
L0.617 °20.1024 °2-0.2526 °2-0.5563 °2-0.4306 °2--1.0951 °2
S0.0082 Å °0.0502 Å °0.0583 Å °0.0625 Å °0.0136 Å °0.0595 Å °-0.068 Å °-0.0988 Å °-0.0185 Å °
Refinement TLS groupSelection details: all

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