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- PDB-3ib9: Propionyl-CoA Carboxylase Beta Subunit, D422L -

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Basic information

Entry
Database: PDB / ID: 3ib9
TitlePropionyl-CoA Carboxylase Beta Subunit, D422L
ComponentsPropionyl-CoA carboxylase complex B subunit
KeywordsBIOSYNTHETIC PROTEIN / 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 / Streptomces / Streptomyces coelicolor / Biotin
Function / homology
Function and homology information


propionyl-CoA carboxylase activity / 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 / ClpP/crotonase-like domain superfamily ...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
BIOTIN / Propionyl-CoA carboxylase complex B subunit
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDiacovich, L. / Arabolaza, A. / Shillito, E.M. / Lin, T.-W. / Mitchell, D.L. / Pham, H. / 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
DepositionJul 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propionyl-CoA carboxylase complex B subunit
B: Propionyl-CoA carboxylase complex B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1256
Polymers114,4442
Non-polymers6814
Water6,107339
1
A: Propionyl-CoA carboxylase complex B subunit
B: Propionyl-CoA carboxylase complex B subunit
hetero molecules

A: Propionyl-CoA carboxylase complex B subunit
B: Propionyl-CoA carboxylase complex B subunit
hetero molecules

A: Propionyl-CoA carboxylase complex B subunit
B: Propionyl-CoA carboxylase complex B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,37618
Polymers343,3336
Non-polymers2,04212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area47970 Å2
ΔGint-348 kcal/mol
Surface area99790 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-95 kcal/mol
Surface area39190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.494, 168.494, 80.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Propionyl-CoA carboxylase complex B subunit


Mass: 57222.234 Da / Num. of mol.: 2 / Mutation: D422L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3 / Gene: pccB, SCK13.18c, SCO4926 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X4K7
#2: Chemical ChemComp-BTN / BIOTIN / Biotin


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris, 2.0M (NH4)SO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2006 / Details: Flat Mirror, Rh coated
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 96304 / Redundancy: 8.9 %
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.274 3340 3.8 %
Rwork0.246 --
obs-66428 75.7 %
Solvent computationBsol: 62.593 Å2
Displacement parametersBiso max: 114.49 Å2 / Biso mean: 34.83 Å2 / Biso min: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1--3.829 Å20 Å20 Å2
2---3.829 Å20 Å2
3---7.657 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7904 0 42 339 8285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.287
X-RAY DIFFRACTIONc_mcbond_it1.2221.5
X-RAY DIFFRACTIONc_scbond_it2.0012
X-RAY DIFFRACTIONc_mcangle_it1.8342
X-RAY DIFFRACTIONc_scangle_it2.8642.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5btn.parbtn.top

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