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- PDB-2f9y: The Crystal Structure of The Carboxyltransferase Subunit of ACC f... -

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Basic information

Entry
Database: PDB / ID: 2f9y
TitleThe Crystal Structure of The Carboxyltransferase Subunit of ACC from Escherichia coli
Components
  • Acetyl-CoA carboxylase, Carboxyltransferase alpha chain
  • Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
KeywordsLIGASE / zinc ribbon / crotonase superfamily / spiral domain
Function / homology
Function and homology information


acetate CoA-transferase complex / acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / negative regulation of translation / mRNA binding ...acetate CoA-transferase complex / acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / negative regulation of translation / mRNA binding / DNA binding / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / 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, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBilder, P.W.
CitationJournal: Biochemistry / Year: 2006
Title: The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-Binding Motif Unique to the Bacterial Enzyme(,).
Authors: Bilder, P. / Lightle, S. / Bainbridge, G. / Ohren, J. / Finzel, B. / Sun, F. / Holley, S. / Al-Kassim, L. / Spessard, C. / Melnick, M. / Newcomer, M. / Waldrop, G.L.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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, Carboxyltransferase alpha chain
B: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9323
Polymers70,8672
Non-polymers651
Water1267
1
A: Acetyl-CoA carboxylase, Carboxyltransferase alpha chain
B: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules

A: Acetyl-CoA carboxylase, Carboxyltransferase alpha chain
B: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8656
Polymers141,7344
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area12490 Å2
ΔGint-94 kcal/mol
Surface area42980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.729, 156.728, 192.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the transformation -y, -x, -z+1/6

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Components

#1: Protein Acetyl-CoA carboxylase, Carboxyltransferase alpha chain /


Mass: 37502.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pCZB4(pET14) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3pLysS
References: GenBank: 4902926, UniProt: P0ABD5*PLUS, acetyl-CoA carboxylase
#2: Protein Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / ACCase beta chain


Mass: 33363.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: accD / Plasmid: pCZB4(pET14) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3pLysS
References: UniProt: P0A9Q6, UniProt: P0A9Q5*PLUS, acetyl-CoA carboxylase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.82 Å3/Da / Density % sol: 74.49 %
Crystal growTemperature: 277 K / pH: 9.5
Details: 1M NaH2PO4, 1M K2HPO4, 2M Li2SO4, 1M CAPS, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 9.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorDate: Jan 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNumber: 23565 / Rmerge(I) obs: 0.068 / Χ2: 0.896 / D res high: 3.2 Å / D res low: 30 Å / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.873098.510.0381.307
5.466.8799.810.0511.13
4.785.4610010.0561.138
4.344.7810010.0581.212
4.034.3410010.0751.014
3.794.0310010.10.811
3.63.7910010.1390.715
3.453.610010.1950.605
3.313.4510010.2810.549
3.23.3110010.4120.493
ReflectionResolution: 3.2→30 Å / Num. obs: 23565 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 0 Å2 / Rsym value: 0.068 / Net I/σ(I): 26.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 8 % / Mean I/σ(I) obs: 8 / Rsym value: 0.412 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.573 / Cor.coef. Fo:Fc: 0.506
Highest resolutionLowest resolution
Translation4 Å29.73 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F9I

2f9i


Resolution: 3.2→29.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 232301.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2247 10 %RANDOM
Rwork0.257 ---
obs0.257 22466 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.13 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 79.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.46 Å211.77 Å20 Å2
2---5.46 Å20 Å2
3---10.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 1 7 4266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it12.71.5
X-RAY DIFFRACTIONc_mcangle_it19.82
X-RAY DIFFRACTIONc_scbond_it26.12
X-RAY DIFFRACTIONc_scangle_it32.42.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 366 10.4 %
Rwork0.367 3140 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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