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- PDB-5csk: Crystal structure of yeast acetyl-CoA carboxylase, unbiotinylated -

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Basic information

Entry
Database: PDB / ID: 5csk
TitleCrystal structure of yeast acetyl-CoA carboxylase, unbiotinylated
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 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 1.1Sep 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)497,9352
Polymers497,9352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.879, 159.879, 615.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115B22 - 568
2115A22 - 568
1124A574 - 695
2124B574 - 695
1224A798 - 2200
2224B798 - 2200

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.871157, 0.006153, -0.490967), (0.013498, -0.999844, 0.011419), (-0.49082, -0.016574, -0.871104)133.336441, 199.565903, 510.582489
3given(1), (1), (1)
4given(0.868341, -0.128308, -0.479083), (-0.127195, -0.991262, 0.034939), (-0.47938, 0.030598, -0.877074)143.711716, 190.453201, 508.547424

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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

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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: 3.95 Å3/Da / Density % sol: 68.86 %
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: Jul 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 136014 / % possible obs: 93.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.085 / Rrim(I) all: 0.127 / Χ2: 1.065 / Net I/av σ(I): 8.257 / Net I/σ(I): 6.4 / Num. measured all: 307202
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.1-3.212.30.881130070.4520.681.0290.5
3.21-3.342.30.612132360.6230.4711.0391.70.776
3.34-3.492.30.431135130.7780.3281.04893.90.544
3.49-3.682.30.277133890.8820.2151.04592.80.353
3.68-3.912.30.188135480.9420.1461.07893.20.24
3.91-4.212.30.13133910.9690.11.08992.40.165
4.21-4.632.30.09138090.9820.0711.16494.90.115
4.63-5.32.20.077138060.9840.0621.19394.20.099
5.3-6.672.20.07140660.9880.0561.08494.80.09
6.67-502.20.036142490.9960.0290.89292.20.046

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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: AC1-2 AC3-5 BT-BCCP-AC1-5

Resolution: 3.1→49.47 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.888 / SU B: 20.62 / SU ML: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.86 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY TENTATIVE SEGMENT. THE ACTUAL RESIDUE ASSIGNMENT FOR SEGMENT 1154-1162 IN CHAIN B IS TENTATIVE DUE TO NO LARGE SIDE CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 6831 5 %RANDOM
Rwork0.2167 ---
obs0.2199 129166 93.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 255.59 Å2 / Biso mean: 92.666 Å2 / Biso min: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2--2.58 Å2-0 Å2
3----5.16 Å2
Refinement stepCycle: final / Resolution: 3.1→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31806 0 0 0 31806
Num. residues----4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01932472
X-RAY DIFFRACTIONr_bond_other_d0.0020.0231249
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9643952
X-RAY DIFFRACTIONr_angle_other_deg0.814371889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40353997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84424.121529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.686155702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.62815227
X-RAY DIFFRACTIONr_chiral_restr0.0750.24897
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02136656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027423
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B3169MEDIUM POSITIONAL0.770.5
1B5101LOOSE POSITIONAL0.875
1B3169MEDIUM THERMAL20.792
1B5101LOOSE THERMAL20.0210
2A22536MEDIUM POSITIONAL0.670.5
2A22536MEDIUM THERMAL10.582
LS refinement shellResolution: 3.096→3.263 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.387 960 -
Rwork0.313 18127 -
all-19087 -
obs--90.76 %

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