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- PDB-3mfm: Crystal Structures and Mutational Analyses of Acyl-CoA Carboxylas... -

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Basic information

Entry
Database: PDB / ID: 3mfm
TitleCrystal Structures and Mutational Analyses of Acyl-CoA Carboxylase Subunit of Streptomyces coelicolor
ComponentsPropionyl-CoA carboxylase complex B subunit
KeywordsLIGASE / ACCase / PCCase / ACC / PCC / Propionyl-CoA / CT / Carboxyltransferase / Polyketide / Fatty Acid / PKS / FAS / Polyketide Synthase / Fatty Acid Synthase / Carboxylase / beta subunit / PccB / Acyl-CoA / Acyl-CoA Carboxylase / Biotin
Function / homology
Function and homology information


acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process
Similarity search - Function
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 ...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
Propionyl-CoA carboxylase complex B subunit
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsDiacovich, L. / Arabolaza, A. / Shillito, E.M. / Lin, T.-W. / Mitchell, D.L. / Melgar, M.M.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structures and mutational analyses of acyl-CoA carboxylase beta subunit of Streptomyces coelicolor.
Authors: Arabolaza, A. / Shillito, M.E. / Lin, T.W. / Diacovich, L. / Melgar, M. / Pham, H. / Amick, D. / Gramajo, H. / Tsai, S.C.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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

Downloads & links

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Assembly

Deposited unit
C: Propionyl-CoA carboxylase complex B subunit
F: Propionyl-CoA carboxylase complex B subunit
A: Propionyl-CoA carboxylase complex B subunit
B: Propionyl-CoA carboxylase complex B subunit
D: Propionyl-CoA carboxylase complex B subunit
E: Propionyl-CoA carboxylase complex B subunit


Theoretical massNumber of molelcules
Total (without water)343,3396
Polymers343,3396
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45410 Å2
ΔGint-239 kcal/mol
Surface area100220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.668, 220.961, 136.742
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Propionyl-CoA carboxylase complex B subunit


Mass: 57223.180 Da / Num. of mol.: 6 / Mutation: D422N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: pccB, SCK13.18c, SCO4926 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4K7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M Bis-TrispH 6.8, 10% MPD, 0.2M Ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2005
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 182058 / % possible obs: 99 % / Observed criterion σ(F): 2.38 / Observed criterion σ(I): 2.38 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.75

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Processing

Software
NameVersionClassification
PHENIX1.6.1_357refinement
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→38.824 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU ML: 0.37 / σ(F): 1.89 / Phase error: 32.6 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2684 9099 5.01 %
Rwork0.2242 --
obs0.2265 181735 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.693 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.7055 Å2-0 Å22.2597 Å2
2--1.37 Å2-0 Å2
3---21.3355 Å2
Refinement stepCycle: LAST / Resolution: 2.38→38.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23718 0 0 0 23718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924198
X-RAY DIFFRACTIONf_angle_d1.20832880
X-RAY DIFFRACTIONf_dihedral_angle_d16.1998796
X-RAY DIFFRACTIONf_chiral_restr0.0773708
X-RAY DIFFRACTIONf_plane_restr0.0054404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4630.33678990.266216827X-RAY DIFFRACTION97
2.463-2.56160.32898830.254817312X-RAY DIFFRACTION99
2.5616-2.67820.31929440.246617238X-RAY DIFFRACTION99
2.6782-2.81930.31169030.239817240X-RAY DIFFRACTION99
2.8193-2.99590.29059080.236617370X-RAY DIFFRACTION99
2.9959-3.22710.29068730.236417466X-RAY DIFFRACTION100
3.2271-3.55170.27929240.230717405X-RAY DIFFRACTION100
3.5517-4.06520.25579610.212217322X-RAY DIFFRACTION99
4.0652-5.11980.23428800.187617423X-RAY DIFFRACTION99
5.1198-38.82910.2229240.201117033X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 136.1564 Å / Origin y: -63.2124 Å / Origin z: 99.2388 Å
111213212223313233
T0.1869 Å2-0.0018 Å2-0.03 Å2--0.0216 Å20.0143 Å2---0.0529 Å2
L2.9836 °20.063 °2-0.0378 °2-0.0373 °2-0.0005 °2--0.1293 °2
S-0.1393 Å °-0.0081 Å °0.3903 Å °-0.0107 Å °0.0735 Å °0.0147 Å °0.0344 Å °-0.005 Å °-0.0032 Å °
Refinement TLS groupSelection details: all

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