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- PDB-5cs4: Crystal structure of domains AC3-AC5 of yeast acetyl-CoA carboxylase -

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Basic information

Entry
Database: PDB / ID: 5cs4
TitleCrystal structure of domains AC3-AC5 of yeast acetyl-CoA carboxylase
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE / acetyl-CoA carboxylase
Function / homology
Function and homology information


: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / 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 / fatty acid biosynthetic process / protein import into nucleus / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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 ...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 / 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.
Similarity search - Domain/homology
Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.19 Å
AuthorsWei, J. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD012018 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK067238 United States
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer.
Authors: Wei, J. / Tong, L.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)108,0542
Polymers108,0542
Non-polymers00
Water00
1
A: Acetyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)54,0271
Polymers54,0271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-CoA carboxylase


Theoretical massNumber of molelcules
Total (without water)54,0271
Polymers54,0271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-6 kcal/mol
Surface area38040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.849, 93.285, 111.144
Angle α, β, γ (deg.)90.000, 100.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetyl-CoA carboxylase / ACC / Fatty acid synthetase 3 / mRNA transport-defective protein 7


Mass: 54026.934 Da / Num. of mol.: 2 / Fragment: unp residues 1036-1503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ACC1, ABP2, FAS3, MTR7, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase

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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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80 mM HEPES (pH 7.5), 4 % (v/v) MPD, 8 mM sodium citrate, 4% (v/v) glycerol, and 40mM NDSB-201

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 19141 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.08 / Χ2: 1.05 / Net I/av σ(I): 21.875 / Net I/σ(I): 11.1 / Num. measured all: 144655
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.317.60.40518920.9650.1560.4341.068100
3.31-3.457.60.27918870.9840.1080.2991.045100
3.45-3.67.60.17919210.9920.070.1921.004100
3.6-3.797.60.14219220.9950.0550.1531.025100
3.79-4.037.60.10118820.9970.0390.1081.028100
4.03-4.347.60.07819130.9980.030.0841.005100
4.34-4.787.50.07319310.9970.0290.0781.007100
4.78-5.477.50.06919010.9980.0270.0741.032100
5.47-6.897.30.06719260.9980.0270.0721.077100
6.89-507.50.05119660.9990.020.0551.20899.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.19→42.9 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / SU B: 27.385 / SU ML: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 980 5.1 %RANDOM
Rwork0.2335 ---
obs0.2362 18134 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.96 Å2 / Biso mean: 79.69 Å2 / Biso min: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.41 Å2
2--0.46 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 3.19→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6353 0 0 0 6353
Num. residues----787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196476
X-RAY DIFFRACTIONr_bond_other_d0.0040.026288
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9668773
X-RAY DIFFRACTIONr_angle_other_deg0.77314424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51923.849317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.888151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4481552
X-RAY DIFFRACTIONr_chiral_restr0.0690.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021498
X-RAY DIFFRACTIONr_mcbond_it5.2767.793138
X-RAY DIFFRACTIONr_mcbond_other5.2757.793137
X-RAY DIFFRACTIONr_mcangle_it8.41711.6713905
LS refinement shellResolution: 3.19→3.362 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4 160 -
Rwork0.337 2584 -
all-2744 -
obs--99.17 %

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