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

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Basic information

Entry
Database: PDB / ID: 3gid
TitleThe biotin carboxylase (BC) domain of human Acetyl-CoA Carboxylase 2 (ACC2) in complex with Soraphen A
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
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 / positive regulation of lipid storage / intracellular glutamate homeostasis / 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
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 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. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SORAPHEN A / Acetyl-CoA carboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase 2
B: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2274
Polymers120,1862
Non-polymers1,0412
Water3,549197
1
A: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6142
Polymers60,0931
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6142
Polymers60,0931
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.339, 141.000, 123.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 60092.949 Da / Num. of mol.: 2 / Fragment: BC domain (UNP residues 238-760)
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: Chemical ChemComp-S1A / SORAPHEN A


Mass: 520.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H44O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.8 M NA FORMATE PH 8.5, 5 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→26.8 Å / Num. all: 51849 / Num. obs: 51849 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 27
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5006

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Processing

Software
NameClassification
CrystalCleardata collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 372757.59 / 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
Rfree0.242 2533 5 %RANDOM
Rwork0.2 ---
all0.202 50203 --
obs0.202 50203 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4095 Å2 / ksol: 0.38851 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20 Å2
2---1.37 Å20 Å2
3----0.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7142 0 74 197 7413
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it2.281.5
X-RAY DIFFRACTIONc_mcangle_it3.222
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 389 5.1 %
Rwork0.252 7246 -
obs-7246 85.9 %

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