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- PDB-3glk: The biotin carboxylase (BC) domain of human Acetyl-CoA Carboxylas... -

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Basic information

Entry
Database: PDB / ID: 3glk
TitleThe biotin carboxylase (BC) domain of human Acetyl-CoA Carboxylase 2 (ACC2)
ComponentsAcetyl-CoA carboxylase 2
KeywordsLIGASE / ATP binding / carboxylase / ATP-binding / Biotin / Fatty acid biosynthesis / Lipid synthesis / Manganese / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein / ACC2-BC
Function / homology
Function and homology information


intracellular aspartate homeostasis / lactic acid secretion / mitochondrial fatty acid beta-oxidation multienzyme complex / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of heart growth / Biotin transport and metabolism / acetyl-CoA carboxylase / negative regulation of fatty acid beta-oxidation / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process ...intracellular aspartate homeostasis / lactic acid secretion / mitochondrial fatty acid beta-oxidation multienzyme complex / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of heart growth / Biotin transport and metabolism / acetyl-CoA carboxylase / negative regulation of fatty acid beta-oxidation / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / tricarboxylic acid metabolic process / acetyl-CoA carboxylase activity / ChREBP activates metabolic gene expression / intracellular glutamate homeostasis / positive regulation of lipid storage / Carnitine metabolism / pentose-phosphate shunt / biotin binding / glucose import / fatty acid oxidation / regulation of glucose metabolic process / energy homeostasis / response to nutrient / Activation of gene expression by SREBF (SREBP) / response to organic cyclic compound / fatty acid biosynthetic process / protein homotetramerization / mitochondrial outer membrane / response to xenobiotic stimulus / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / 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 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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / Single hybrid motif / ATP-grasp fold, A domain / 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
Acetyl-CoA carboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPrice, A. / Kulathila, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Synthesis and characterization of a BODIPY-labeled derivative of Soraphen A that binds to acetyl-CoA carboxylase.
Authors: Raymer, B. / Kavana, M. / Price, A. / Wang, B. / Corcoran, L. / Kulathila, R. / Groarke, J. / Mann, T.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase 2


Theoretical massNumber of molelcules
Total (without water)60,0931
Polymers60,0931
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.536, 97.536, 127.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Acetyl-CoA carboxylase 2 / / ACC-beta / Biotin carboxylase


Mass: 60092.949 Da / Num. of mol.: 1 / Fragment: BC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACACB, ACC2, ACCB / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODONPLUS (DE3)
References: UniProt: O00763, acetyl-CoA carboxylase, biotin carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS, 0.1M MG FORMATE, 20% PEG 4K, 15% GLYCEROL, 5 MM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→33.3 Å / Num. all: 35837 / Num. obs: 35837 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 28.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3475

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Processing

Software
NameClassification
CrystalCleardata collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 371532.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2060 6 %RANDOM
Rwork0.212 ---
obs0.212 34542 94.6 %-
all-34542 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5716 Å2 / ksol: 0.37705 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 0 289 3935
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.732.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 338 6.3 %
Rwork0.226 5034 -
obs-5372 89.8 %

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