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- PDB-6f7v: Crystal structure of LkcE E64Q mutant in complex with LC-KA05 -

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Basic information

Entry
Database: PDB / ID: 6f7v
TitleCrystal structure of LkcE E64Q mutant in complex with LC-KA05
ComponentsLkcE
KeywordsFLAVOPROTEIN / Amine oxydase / cyclase / Post-PKS enzyme / tayloring enzyme
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-CWH / FLAVIN-ADENINE DINUCLEOTIDE / LkcE
Similarity search - Component
Biological speciesStreptomyces rochei subsp. volubilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.03 Å
AuthorsDorival, J. / Risser, F. / Jacob, C. / Collin, S. / Drager, G. / Kirschning, A. / Paris, C. / Chagot, B. / Gruez, A. / Weissman, K.J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyPKS-PPIs / AAP JCJC SVS3 8 2011 France
CitationJournal: Nat Commun / Year: 2018
Title: Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis.
Authors: Dorival, J. / Risser, F. / Jacob, C. / Collin, S. / Drager, G. / Paris, C. / Chagot, B. / Kirschning, A. / Gruez, A. / Weissman, K.J.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LkcE
B: LkcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4278
Polymers98,6932
Non-polymers2,7356
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-26 kcal/mol
Surface area32200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.834, 124.834, 157.392
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-502-

CA

21A-660-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LkcE / Amine oxidase


Mass: 49346.332 Da / Num. of mol.: 2 / Mutation: E64Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rochei subsp. volubilis (bacteria)
Gene: lkcE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G4V2H3, monoamine oxidase

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Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CWH / [(2~{S},5~{R},8~{S},11~{S})-1-[(2~{R},3~{R},5~{R},6~{S})-3,5-dimethyl-6-oxidanyl-4-oxidanylidene-oxan-2-yl]-5,11-dimeth yl-8-oxidanyl-13-[[(2~{S})-2-oxidanylpropanoyl]amino]tridecan-2-yl] ethanoate / LC-KA05


Mass: 515.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H49NO8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16 % PEG 8000, 160 mM calcium acetate, Bis Tris 100 mM pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 3.03→48.9 Å / Num. obs: 24814 / % possible obs: 99.8 % / Redundancy: 29.7 % / CC1/2: 1 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.021 / Rrim(I) all: 0.113 / Net I/σ(I): 28 / Num. measured all: 737003
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.03-3.1127.90.7617570.940.1420.77497.2
13.55-48.922.50.03534010.0070.03698.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.03→48 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 17.082 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1170 4.7 %RANDOM
Rwork0.1912 ---
obs0.1938 23588 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164 Å2 / Biso mean: 68.666 Å2 / Biso min: 30.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å2-0 Å2-0 Å2
2--2.11 Å2-0 Å2
3----4.22 Å2
Refinement stepCycle: final / Resolution: 3.03→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6801 0 185 136 7122
Biso mean--69.48 52.89 -
Num. residues----861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197177
X-RAY DIFFRACTIONr_bond_other_d0.0040.026424
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9739751
X-RAY DIFFRACTIONr_angle_other_deg1.1293.00514888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07923.448348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.776151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9731552
X-RAY DIFFRACTIONr_chiral_restr0.0850.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021530
LS refinement shellResolution: 3.031→3.109 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 81 -
Rwork0.286 1672 -
all-1753 -
obs--97.23 %

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