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- PDB-5ini: Structural basis for acyl-CoA carboxylase-mediated assembly of un... -

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Basic information

Entry
Database: PDB / ID: 5ini
TitleStructural basis for acyl-CoA carboxylase-mediated assembly of unusual polyketide synthase extender units incorporated into the stambomycin antibiotics
ComponentsPutative carboxyl transferase
KeywordsTRANSFERASE / Polyketide / Acyl-CoA / Crotonase / Extender-Unit
Function / homology
Function and homology information


propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / transferase activity
Similarity search - Function
Acetyl-CoA carboxylase carboxyl transferase, beta subunit / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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
HEXANOYL-COENZYME A / Putative carboxyl transferase
Similarity search - Component
Biological speciesStreptomyces ambofaciens ATCC 23877 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsValentic, T.R. / Ray, L. / Miyazawa, T. / Withall, D.M. / Song, L. / Milligan, J.C. / Osada, H. / Tsai, S.C. / Challis, G.L.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)doctoral training grant United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100305 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM076330 United States
CitationJournal: Nat Commun / Year: 2016
Title: A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units.
Authors: Ray, L. / Valentic, T.R. / Miyazawa, T. / Withall, D.M. / Song, L. / Milligan, J.C. / Osada, H. / Takahashi, S. / Tsai, S.C. / Challis, G.L.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative carboxyl transferase
B: Putative carboxyl transferase
C: Putative carboxyl transferase
D: Putative carboxyl transferase
E: Putative carboxyl transferase
F: Putative carboxyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,06710
Polymers348,6046
Non-polymers3,4634
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47390 Å2
ΔGint-239 kcal/mol
Surface area92590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.978, 161.526, 187.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative carboxyl transferase / Putative propionyl-CoA carboxylase


Mass: 58100.641 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ambofaciens ATCC 23877 (bacteria)
Gene: SAM23877_7108, SAMR0483 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0ACI9
#2: Chemical
ChemComp-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.41 Å3/Da / Density % sol: 48.91 % / Description: Rod shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 26-32% PEG 5000 MME, 0.2 M ammonium sulfate and 0.1 M MES pH 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2015
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→58.245 Å / Num. obs: 79293 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.206 / Net I/σ(I): 10
Reflection shellResolution: 2.85→2.91 Å / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ING

5ing


Resolution: 2.85→58.233 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 2000 2.53 %
Rwork0.1731 --
obs0.1746 79174 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→58.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22284 0 220 392 22896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722978
X-RAY DIFFRACTIONf_angle_d0.89431244
X-RAY DIFFRACTIONf_dihedral_angle_d14.50713633
X-RAY DIFFRACTIONf_chiral_restr0.0543489
X-RAY DIFFRACTIONf_plane_restr0.0054102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.92130.30371410.21655452X-RAY DIFFRACTION100
2.9213-3.00030.28471400.20145408X-RAY DIFFRACTION100
3.0003-3.08860.2971420.19735468X-RAY DIFFRACTION100
3.0886-3.18830.281410.19875459X-RAY DIFFRACTION100
3.1883-3.30220.26041420.19465454X-RAY DIFFRACTION100
3.3022-3.43440.25881410.17815464X-RAY DIFFRACTION100
3.4344-3.59070.23911420.16895474X-RAY DIFFRACTION100
3.5907-3.780.23691430.16245484X-RAY DIFFRACTION100
3.78-4.01670.18271410.15815486X-RAY DIFFRACTION100
4.0167-4.32680.19641430.1495509X-RAY DIFFRACTION100
4.3268-4.7620.19931440.13475548X-RAY DIFFRACTION100
4.762-5.45060.20271430.16115548X-RAY DIFFRACTION100
5.4506-6.86550.22451460.19115612X-RAY DIFFRACTION100
6.8655-58.24510.21311510.18565808X-RAY DIFFRACTION100

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