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- PDB-3h0s: Crystal structure of the carboxyltransferase domain of acetyl-coe... -

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Basic information

Entry
Database: PDB / ID: 3h0s
TitleCrystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with compound 7
ComponentsAcetyl-CoA carboxylase
KeywordsTRANSFERASE / ACETYL-COA CARBOXYLASE / CARBOXYLTRANSFERASE / INHIBITOR / ACC / CT / ATP-binding / Biotin / Cytoplasm / Fatty acid biosynthesis / Ligase / Lipid synthesis / Metal-binding / Multifunctional enzyme / Nucleotide-binding
Function / homology
Function and homology information


Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / long-chain fatty acid biosynthetic process / protein import into nucleus / fatty acid biosynthetic process / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal ...ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / 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 / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-B38 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsVajdos, F.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Discovery of small molecule isozyme non-specific inhibitors of mammalian acetyl-CoA carboxylase 1 and 2.
Authors: Corbett, J.W. / Freeman-Cook, K.D. / Elliott, R. / Vajdos, F. / Rajamohan, F. / Kohls, D. / Marr, E. / Zhang, H. / Tong, L. / Tu, M. / Murdande, S. / Doran, S.D. / Houser, J.A. / Song, W. / ...Authors: Corbett, J.W. / Freeman-Cook, K.D. / Elliott, R. / Vajdos, F. / Rajamohan, F. / Kohls, D. / Marr, E. / Zhang, H. / Tong, L. / Tu, M. / Murdande, S. / Doran, S.D. / Houser, J.A. / Song, W. / Jones, C.J. / Coffey, S.B. / Buzon, L. / Minich, M.L. / Dirico, K.J. / Tapley, S. / McPherson, R.K. / Sugarman, E. / Harwood, H.J. / Esler, W.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,1289
Polymers261,7143
Non-polymers1,4146
Water43,2902403
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4196
Polymers174,4762
Non-polymers9434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12180 Å2
ΔGint-127 kcal/mol
Surface area57690 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4196
Polymers174,4762
Non-polymers9434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-126 kcal/mol
Surface area53590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.716, 121.678, 145.991
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acetyl-CoA carboxylase / ACC / Biotin carboxylase


Mass: 87237.977 Da / Num. of mol.: 3 / Fragment: Residues 1476-2233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FAS3, ACC1, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-B38 / 1'-(1H-indazol-7-ylcarbonyl)-6-methylspiro[chromene-2,4'-piperidin]-4(3H)-one


Mass: 375.420 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H21N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2403 / 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: 4.18 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M Na citrate ,pH 5.5, 200 mM NaCl, 8% PEG8000, 10% glycerol, vapor diffusion, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→40.7 Å / Num. obs: 159230 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065 / Χ2: 1.271 / Net I/σ(I): 21.112
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.43-2.523.40.614148791.41491.9
2.52-2.623.40.501157721.498
2.62-2.743.40.386158511.41598.3
2.74-2.883.50.28159441.36798.4
2.88-3.063.50.193159351.37598.8
3.06-3.33.60.128159901.34999
3.3-3.633.60.074160521.32599.3
3.63-4.153.60.043161391.21499.5
4.15-5.233.60.027162350.99499.7
5.23-503.60.022164330.92499.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W2X

1w2x


Resolution: 2.43→40.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.848 / SU B: 6.065 / SU ML: 0.138 / SU R Cruickshank DPI: 0.213 / SU Rfree: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 15829 9.9 %RANDOM
Rwork0.16 ---
obs0.166 159203 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 164.91 Å2 / Biso mean: 56.371 Å2 / Biso min: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.24 Å2
2--2.86 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.43→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16257 0 110 2403 18770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02216739
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215215
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.96322693
X-RAY DIFFRACTIONr_angle_other_deg1.035335294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.79852032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3823.765810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.642152853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.67215138
X-RAY DIFFRACTIONr_chiral_restr0.1280.22438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023518
X-RAY DIFFRACTIONr_nbd_refined0.2320.24310
X-RAY DIFFRACTIONr_nbd_other0.210.217270
X-RAY DIFFRACTIONr_nbtor_refined0.1880.28045
X-RAY DIFFRACTIONr_nbtor_other0.0960.210143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.21875
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.180.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.2187
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3610.253
X-RAY DIFFRACTIONr_mcbond_it1.3021.511094
X-RAY DIFFRACTIONr_mcbond_other0.2411.54154
X-RAY DIFFRACTIONr_mcangle_it1.938216331
X-RAY DIFFRACTIONr_scbond_it2.47537480
X-RAY DIFFRACTIONr_scangle_it3.7184.56362
LS refinement shellResolution: 2.43→2.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 1080 -
Rwork0.23 10018 -
all-11098 -
obs--93.12 %

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