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- PDB-5csl: Crystal structure of the 500 kD yeast acetyl-CoA carboxylase holo... -

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Basic information

Entry
Database: PDB / ID: 5csl
TitleCrystal structure of the 500 kD yeast acetyl-CoA carboxylase holoenzyme dimer
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 / biotin carboxylase activity / acetyl-CoA carboxylase complex ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase complex / 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 / 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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / 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
Chem-BTI / COENZYME A / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsWei, J. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD012018 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK067238 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 / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,9266
Polymers497,9352
Non-polymers1,9924
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22190 Å2
ΔGint-78 kcal/mol
Surface area171720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.866, 159.866, 614.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 248967.391 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O2S
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 14% (w/v) PEG3350, 4% (v/v) tert-butanol, and 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 129365 / % possible obs: 97.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.099 / Rrim(I) all: 0.168 / Χ2: 1.039 / Net I/av σ(I): 7.032 / Net I/σ(I): 5.1 / Num. measured all: 389181
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.2-3.312.70.901113720.4480.6331.04387.4
3.31-3.452.90.755126030.540.5151.04496.60.919
3.45-3.63.10.548129150.720.3651.03898.50.662
3.6-3.7930.368128790.8370.2461.02898.20.445
3.79-4.033.10.266129270.9130.1771.01898.50.322
4.03-4.343.10.183131030.9530.1211.03299.20.221
4.34-4.783.10.128130620.9750.0851.0598.70.154
4.78-5.473.10.113131670.9770.0751.057990.137
5.47-6.893.10.103134060.9820.0681.04799.40.124
6.89-502.90.036139310.9980.0241.03998.90.043

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: acetyl-CoA carboxylase unbiotinylated

Resolution: 3.2→49.93 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.334 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TENTATIVE SEGMENT. THE ACTUAL RESIDUE ASSIGNMENT FOR SEGMENT 1153-1161 IN CHAIN B IS TENTATIVE DUE TO NO LARGE SIDE CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.26579 6469 5 %RANDOM
Rwork0.21904 ---
obs0.22137 122246 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.326 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2--2.25 Å2-0 Å2
3----4.5 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32651 0 126 0 32777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01933451
X-RAY DIFFRACTIONr_bond_other_d0.0020.0232200
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.96545293
X-RAY DIFFRACTIONr_angle_other_deg0.824374090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33454101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91124.1751564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315155862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.43415231
X-RAY DIFFRACTIONr_chiral_restr0.0750.25056
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02137660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027614
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.373 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 899 -
Rwork0.334 16119 -
obs--89.55 %

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