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- PDB-1od2: Acetyl-CoA Carboxylase Carboxyltransferase Domain -

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Basic information

Entry
Database: PDB / ID: 1od2
TitleAcetyl-CoA Carboxylase Carboxyltransferase Domain
ComponentsACETYL-COENZYME A CARBOXYLASE
KeywordsLIGASE / ACC / ACETYL-COA / ACETYL-COA CARBOXYLASE / OBESITY
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 / biotin carboxylase activity / acetyl-CoA carboxylase complex ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / long-chain fatty acid biosynthetic process / protein import into nucleus / fatty acid biosynthetic process / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / 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-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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / 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
ACETYL COENZYME *A / ADENINE / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZhang, H. / Yang, Z. / Shen, Y. / Tong, L.
CitationJournal: Science / Year: 2003
Title: Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase.
Authors: Zhang, H. / Yang, Z. / Shen, Y. / Tong, L.
History
DepositionFeb 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jun 13, 2018Group: Data collection / Database references / Refinement description
Category: citation / diffrn_radiation / refine
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol / _refine.pdbx_method_to_determine_struct

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,9324
Polymers183,9872
Non-polymers9452
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.870, 138.130, 101.400
Angle α, β, γ (deg.)90.00, 114.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.22156, -0.71471, -0.66341), (-0.7099, -0.58463, 0.39276), (-0.66855, 0.38393, -0.6369)
Vector: 23.682, 7.65045, 35.03892)

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Components

#1: Protein ACETYL-COENZYME A CARBOXYLASE / ACC


Mass: 91993.422 Da / Num. of mol.: 2 / Fragment: CARBOXYLTRANSFERASE DOMAIN, RESIDUES 1429-2233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00955, acetyl-CoA carboxylase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH5.5
210 %(w/v)PEG80001reservoir
35 %(v/v)glycerol1reservoir
47 mg/mlprotein1drop
51 mMacetyl-CoA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795
DetectorDate: Jul 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 168936 / % possible obs: 92 % / Redundancy: 2.5 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 7 / % possible all: 81
Reflection
*PLUS
Highest resolution: 2.7 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→28.85 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 6032 10.1 %RANDOM
Rwork0.226 ---
obs0.226 59546 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.5 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20.49 Å2
2---7.3 Å20 Å2
3---9.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11286 0 58 89 11433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 958 10.2 %
Rwork0.296 8456 -
obs--88.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ACO.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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