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- PDB-6sm4: AntF (apo): type II PKS acyl-carrier protein -

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Basic information

Entry
Database: PDB / ID: 6sm4
TitleAntF (apo): type II PKS acyl-carrier protein
ComponentsAcyl carrier protein
KeywordsPROTEIN BINDING / Natural Product Biosynthesis / Polyketides / Minimal PKS System / Anthraquinone / Chain Elongation / Catalysis
Function / homologyPhosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Acyl carrier protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBraeuer, A. / Zhou, Q. / Grammbitter, G.L.C. / Schmalhofer, M. / Ruehl, M. / Kaila, V.R.I. / Bode, H. / Groll, M.
CitationJournal: Nat.Chem. / Year: 2020
Title: Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis.
Authors: Brauer, A. / Zhou, Q. / Grammbitter, G.L.C. / Schmalhofer, M. / Ruhl, M. / Kaila, V.R.I. / Bode, H.B. / Groll, M.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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: Acyl carrier protein
B: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)21,7022
Polymers21,7022
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.700, 58.700, 149.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Acyl carrier protein


Mass: 10850.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: C6H68_21855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S8QL96
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid, 1 M LiCl, 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23127 / % possible obs: 99.2 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.5
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3301 / CC1/2: 0.923 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FAD

2fad


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.303 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 1153 5 %RANDOM
Rwork0.1583 ---
obs0.1584 21891 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.68 Å2 / Biso mean: 37.186 Å2 / Biso min: 20.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å2-0 Å2
2--0.54 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 0 132 1359
Biso mean---51.38 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191247
X-RAY DIFFRACTIONr_bond_other_d0.0010.021133
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.9481685
X-RAY DIFFRACTIONr_angle_other_deg0.89432643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9245153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81726.45262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.42152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
X-RAY DIFFRACTIONr_rigid_bond_restr1.52332379
X-RAY DIFFRACTIONr_sphericity_free24.3425104
X-RAY DIFFRACTIONr_sphericity_bonded9.51352388
LS refinement shellResolution: 1.85→1.897 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 83 -
Rwork0.218 1569 -
all-1652 -
obs--99.7 %

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