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- PDB-3iav: Propionyl-CoA Carboxylase Beta Subunit, D422V -

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Basic information

Entry
Database: PDB / ID: 3iav
TitlePropionyl-CoA Carboxylase Beta Subunit, D422V
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
Propionyl-CoA carboxylase complex B subunit
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 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

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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)114,9938
Polymers114,4162
Non-polymers5766
Water5,765320
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)344,97824
Polymers343,2496
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area49350 Å2
ΔGint-536 kcal/mol
Surface area98680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-158 kcal/mol
Surface area38630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.531, 171.531, 75.068
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: 57208.203 Da / Num. of mol.: 2 / Mutation: D422V
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
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
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: 1.75→50 Å / Num. obs: 113083

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.233 5736 4.5 %
Rwork0.217 --
obs-113083 89.2 %
Solvent computationBsol: 37.378 Å2
Displacement parametersBiso max: 102.31 Å2 / Biso mean: 21.91 Å2 / Biso min: 9.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.573 Å20 Å20 Å2
2---0.573 Å20 Å2
3---1.147 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7904 0 30 320 8254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.264
X-RAY DIFFRACTIONc_mcbond_it1.1161.5
X-RAY DIFFRACTIONc_scbond_it2.0482
X-RAY DIFFRACTIONc_mcangle_it1.6832
X-RAY DIFFRACTIONc_scangle_it2.9962.5
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

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