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- PDB-5lvu: XiaF (apo) from Streptomyces sp. -

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Basic information

Entry
Database: PDB / ID: 5lvu
TitleXiaF (apo) from Streptomyces sp.
ComponentsXiaF protein
KeywordsOXIDOREDUCTASE / detoxification / non-canonical flavin-dependent terpenoid cyclase / xenobiotics-degrading enzyme / indigo / indirubin
Function / homology
Function and homology information


fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / : / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKugel, S. / Baunach, M. / Baer, P. / Ishida-Ito, M. / Sundaram, S. / Xu, Z. / Groll, M. / Hertweck, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
CitationJournal: Nat Commun / Year: 2017
Title: Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification.
Authors: Kugel, S. / Baunach, M. / Baer, P. / Ishida-Ito, M. / Sundaram, S. / Xu, Z. / Groll, M. / Hertweck, C.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4323
Polymers44,2401
Non-polymers1922
Water1,11762
1
A: XiaF protein
hetero molecules

A: XiaF protein
hetero molecules

A: XiaF protein
hetero molecules

A: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,72812
Polymers176,9594
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area15640 Å2
ΔGint-182 kcal/mol
Surface area54210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.540, 166.540, 98.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein XiaF protein


Mass: 44239.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: xiaF / Plasmid: pXU520 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: I7IIA9
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.48 Å3/Da / Density % sol: 72.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 0.1 M HEPES, 0.1 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 25318 / % possible obs: 99.6 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.5
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 4.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JBR

2jbr


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.773 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21759 1265 5 %RANDOM
Rwork0.18223 ---
obs0.18398 24035 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.9 Å20 Å2
2--0.9 Å20 Å2
3----2.93 Å2
Refinement stepCycle: 1 / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 10 62 3026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193023
X-RAY DIFFRACTIONr_bond_other_d0.0010.022866
X-RAY DIFFRACTIONr_angle_refined_deg0.7881.9544123
X-RAY DIFFRACTIONr_angle_other_deg0.68936555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1315392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31922.362127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46815457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511530
X-RAY DIFFRACTIONr_chiral_restr0.040.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
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_it2.276.0641571
X-RAY DIFFRACTIONr_mcbond_other2.2336.0631570
X-RAY DIFFRACTIONr_mcangle_it39.0921962
X-RAY DIFFRACTIONr_mcangle_other39.0931963
X-RAY DIFFRACTIONr_scbond_it2.2646.3611451
X-RAY DIFFRACTIONr_scbond_other2.2566.371443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7449.4412149
X-RAY DIFFRACTIONr_long_range_B_refined3.55448.213389
X-RAY DIFFRACTIONr_long_range_B_other3.38148.1363372
X-RAY DIFFRACTIONr_rigid_bond_restr0.55435888
X-RAY DIFFRACTIONr_sphericity_free23.471538
X-RAY DIFFRACTIONr_sphericity_bonded11.44355854
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 88 -
Rwork0.251 1684 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 53.2099 Å / Origin y: -55.106 Å / Origin z: -1.4247 Å
111213212223313233
T0.0335 Å2-0.0336 Å20.0014 Å2-0.0409 Å20.0027 Å2--0.0046 Å2
L0.0177 °20.0181 °2-0.0542 °2-0.194 °2-0.0771 °2--0.1826 °2
S0.0051 Å °0.0013 Å °0.0022 Å °-0.0197 Å °0.0033 Å °-0.0112 Å °-0.0306 Å °0.0145 Å °-0.0084 Å °

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