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- PDB-1w96: Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme... -

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Basic information

Entry
Database: PDB / ID: 1w96
TitleCrystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A
ComponentsACETYL-COENZYME A CARBOXYLASE
KeywordsLIGASE / OBESITY / DIABETES / FATTY ACID METABOLISM / STRUCTURE-BASED DRUG DESIGN / ALLOSTERIC INHIBITION / POLYKETIDE
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
PreATP-grasp fold / PreATP-grasp domain / 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 ...PreATP-grasp fold / PreATP-grasp domain / 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 / Rossmann fold - #20 / 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 / ATP-grasp fold, A domain / Single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SORAPHEN A / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsShen, Y. / Volrath, S.L. / Weatherly, S.C. / Elich, T.D. / Tong, L.
CitationJournal: Mol.Cell / Year: 2004
Title: A Mechanism for the Potent Inhibition of Eukaryotic Acetyl-Coenzyme a Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product
Authors: Shen, Y. / Volrath, S.L. / Weatherly, S.C. / Elich, T.D. / Tong, L.
History
DepositionOct 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYL-COENZYME A CARBOXYLASE
B: ACETYL-COENZYME A CARBOXYLASE
C: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,5196
Polymers184,9573
Non-polymers1,5623
Water26,0321445
1
A: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1732
Polymers61,6521
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1732
Polymers61,6521
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1732
Polymers61,6521
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.830, 96.520, 139.950
Angle α, β, γ (deg.)90.00, 96.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.34576, 0.81813, 0.45947), (-0.8201, -0.50143, 0.2757), (0.45595, -0.28148, 0.84432)-9.90431, 80.52773, 33.51553
3given(0.32725, -0.82537, -0.46009), (-0.82615, -0.48625, 0.28467), (-0.45867, 0.28694, -0.841)119.09418, 80.04326, 217.49756

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Components

#1: Protein ACETYL-COENZYME A CARBOXYLASE / ACC


Mass: 61652.352 Da / Num. of mol.: 3 / Fragment: BIOTIN CARBOXYLASE DOMAIN, RESIDUES 13-566
Source method: isolated from a genetically manipulated source
Details: POLYKETIDE SORAPHEN A
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00955, acetyl-CoA carboxylase
#2: Chemical ChemComp-S1A / SORAPHEN A


Mass: 520.655 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H44O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1445 / 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: 2.22 Å3/Da / Density % sol: 44.1 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.978994,0.979232, 0.970227
DetectorDate: Mar 30, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9789941
20.9792321
30.9702271
ReflectionResolution: 1.8→29.2 Å / Num. obs: 150099 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 88

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKLdata reduction
HKLdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.2 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 371358.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 11219 7.5 %RANDOM
Rwork0.195 ---
obs0.195 150099 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.7639 Å2 / ksol: 0.376114 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å2-0.3 Å2
2---1.31 Å20 Å2
3----2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12726 0 111 1445 14282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.283 1018 7.5 %
Rwork0.258 12641 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SOR.PARSOR.TOP

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