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- PDB-6qsr: The Dehydratase Heterocomplex ApeI:P from Xenorhabdus doucetiae -

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Basic information

Entry
Database: PDB / ID: 6qsr
TitleThe Dehydratase Heterocomplex ApeI:P from Xenorhabdus doucetiae
Components
  • AMP-dependent synthetase and ligase
  • Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase FabA/FabZ
KeywordsBIOSYNTHETIC PROTEIN / Aryl Polyene Pigment / Biosynthesis / Type II Polyketide Synthase / Dehydration
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / ligase activity / lyase activity
Similarity search - Function
3-hydroxylacyl-(acyl carrier protein) dehydratase, predicted / ApeP dehydratase / Dehydrase, ECs4332, predicted / ApeI dehydratase / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase FabA/FabZ / AMP-dependent synthetase and ligase
Similarity search - Component
Biological speciesXenorhabdus doucetiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGrammbitter, G.L.C. / Schmalhofer, M. / Groll, M. / Bode, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments.
Authors: Grammbitter, G.L.C. / Schmalhofer, M. / Karimi, K. / Shi, Y.M. / Schoner, T.A. / Tobias, N.J. / Morgner, N. / Groll, M. / Bode, H.B.
History
DepositionFeb 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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: AMP-dependent synthetase and ligase
B: Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase FabA/FabZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2433
Polymers34,2202
Non-polymers231
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-33 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.680, 47.770, 42.680
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

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Components

#1: Protein AMP-dependent synthetase and ligase


Mass: 13841.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus doucetiae (bacteria) / Gene: XDD1_3466 / Plasmid: pCDF-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD(DE3) / References: UniProt: A0A068QWX2
#2: Protein Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase FabA/FabZ


Mass: 20378.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-Terminal Strep-TEV-Tag / Source: (gene. exp.) Xenorhabdus doucetiae (bacteria) / Gene: XDD1_3473 / Plasmid: pCDF-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD(DE3)
References: UniProt: A0A068QW34, Lyases; Carbon-oxygen lyases; Hydro-lyases
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.08 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 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: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 23313 / % possible obs: 95.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ESI

3esi


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.059 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23804 1163 5 %RANDOM
Rwork0.19923 ---
obs0.20212 22103 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.667 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.36 Å2
2--0.47 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 1 105 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192196
X-RAY DIFFRACTIONr_bond_other_d0.0020.022030
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9512982
X-RAY DIFFRACTIONr_angle_other_deg0.88434719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44724.231104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11915377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3011512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3922.3051057
X-RAY DIFFRACTIONr_mcbond_other1.392.3011056
X-RAY DIFFRACTIONr_mcangle_it1.5053.4361317
X-RAY DIFFRACTIONr_mcangle_other1.5053.441318
X-RAY DIFFRACTIONr_scbond_it1.8662.9071139
X-RAY DIFFRACTIONr_scbond_other1.8652.911140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6674.1341664
X-RAY DIFFRACTIONr_long_range_B_refined2.58727.4192284
X-RAY DIFFRACTIONr_long_range_B_other2.48427.2362269
X-RAY DIFFRACTIONr_rigid_bond_restr1.05334226
X-RAY DIFFRACTIONr_sphericity_free22.227561
X-RAY DIFFRACTIONr_sphericity_bonded4.30554217
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 84 -
Rwork0.37 1606 -
obs--97.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56760.03740.10650.18490.03840.0338-0.07360.0255-0.0249-0.01850.0542-0.0277-0.02630.01440.01940.0228-0.0027-0.0220.0617-0.01490.073450.380513.5112.7718
20.3024-0.1928-0.07170.1898-0.03350.11480.0087-0.02480.03790.0096-0.0029-0.0194-0.02690.0206-0.00580.0371-0.0068-0.02650.0422-0.00820.0344.280728.935424.6743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B9 - 160

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