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- PDB-3ff6: Human ACC2 CT domain with CP-640186 -

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Basic information

Entry
Database: PDB / ID: 3ff6
TitleHuman ACC2 CT domain with CP-640186
ComponentsAcetyl-CoA carboxylase 2
KeywordsLIGASE / Acetyl CoA Carboxylase / ACC2 / ACC / metabolic disorder / fatty acid metabolism / 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 / acetyl-CoA carboxylase / Biotin transport and metabolism / negative regulation of fatty acid beta-oxidation / tricarboxylic acid metabolic process / acetyl-CoA metabolic 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 / acetyl-CoA carboxylase / Biotin transport and metabolism / negative regulation of fatty acid beta-oxidation / tricarboxylic acid metabolic process / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / intracellular glutamate homeostasis / positive regulation of lipid storage / pentose-phosphate shunt / Carnitine shuttle / biotin binding / D-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 / nucleus / metal ion binding / cytosol
Similarity search - Function
ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / 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 ...ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / 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 / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 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. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-RCP / Acetyl-CoA carboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsWilliams, S.P. / Madauss, K.P. / Burkhart, W.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The human ACC2 CT-domain C-terminus is required for full functionality and has a novel twist.
Authors: Madauss, K.P. / Burkhart, W.A. / Consler, T.G. / Cowan, D.J. / Gottschalk, W.K. / Miller, A.B. / Short, S.A. / Tran, T.B. / Williams, S.P.
History
DepositionDec 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: 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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: Acetyl-CoA carboxylase 2
D: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,5088
Polymers344,5664
Non-polymers1,9424
Water1,58588
1
A: Acetyl-CoA carboxylase 2
B: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,2544
Polymers172,2832
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-119 kcal/mol
Surface area59450 Å2
MethodPISA
2
C: Acetyl-CoA carboxylase 2
D: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,2544
Polymers172,2832
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-120 kcal/mol
Surface area58780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.545, 168.836, 293.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 86141.445 Da / Num. of mol.: 4 / Fragment: carboxytransferase domain, UNP residues 1693-2450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACACB, ACC2, ACCB / Plasmid: pACC2_4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O00763, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical
ChemComp-RCP / (3R)-1'-(9-ANTHRYLCARBONYL)-3-(MORPHOLIN-4-YLCARBONYL)-1,4'-BIPIPERIDINE


Mass: 485.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H35N3O3 / Details: Organic Synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 25% Peg 3350, 5% glycerol, and 0.2M Tri-Ammonium Citrate pH 7.0, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM11
SYNCHROTRONAPS 23-ID-D21
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJul 28, 2006
MARMOSAIC 225 mm CCD2CCDOct 19, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→20 Å / Num. all: 62302 / Num. obs: 59688 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.1
Reflection shellResolution: 3.19→3.27 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3407 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human ACC2(1695-2449) from a complex with CP-640188

Resolution: 3.19→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.834 / SU B: 48.73 / SU ML: 0.368 / SU R Cruickshank DPI: 0.413 / SU Rfree: 0.52 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.518 / Stereochemistry target values: Engh & Huber
Details: TLS plus restrained conjugate gradient minimization with a maximum likelihood target.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4710 7.3 %RANDOM
Rwork0.197 ---
all0.201 67270 --
obs0.201 64398 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.34 Å2 / Biso mean: 38.108 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 3.19→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22757 0 144 88 22989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02223463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215571
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.95931964
X-RAY DIFFRACTIONr_angle_other_deg0.83337855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77952963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13623.517998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.894153629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3715156
X-RAY DIFFRACTIONr_chiral_restr0.0580.23559
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024886
X-RAY DIFFRACTIONr_mcbond_it0.2411.514775
X-RAY DIFFRACTIONr_mcbond_other0.0281.56023
X-RAY DIFFRACTIONr_mcangle_it0.461223609
X-RAY DIFFRACTIONr_scbond_it0.60838688
X-RAY DIFFRACTIONr_scangle_it1.0954.58355
LS refinement shellResolution: 3.19→3.271 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 246 -
Rwork0.281 3336 -
all-3582 -
obs-3514 88.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9954-0.5929-0.29721.22250.4731.1161-0.00270.1256-0.1610.0443-0.00460.07170.1966-0.07090.00730.1169-0.0431-0.04610.04730.00840.0661-0.352-1.2311.124
21.0626-0.4234-0.18020.8990.31080.57460.03620.2198-0.0471-0.18030.0342-0.1114-0.03140.0234-0.07050.0943-0.0532-0.00570.12560.01420.066414.09412.196-3.036
31.27360.6117-0.73211.2647-0.52621.14130.0043-0.2291-0.36560.0647-0.0969-0.24610.08550.23570.09260.14370.0183-0.12370.17590.05760.214519.8254.12662.355
41.2170.3512-0.33990.8999-0.26670.50720.107-0.2683-0.02970.2335-0.0380.021-0.09830.0958-0.06910.1998-0.03-0.07990.18740.03220.07627.09221.96572.561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1695 - 2449
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION2B1697 - 2450
4X-RAY DIFFRACTION2B2
5X-RAY DIFFRACTION3C1697 - 2445
6X-RAY DIFFRACTION3C3
7X-RAY DIFFRACTION4D1697 - 2433
8X-RAY DIFFRACTION4D4

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