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- PDB-6x7o: LnmK in complex with 2-sulfonate-propionyl-CoA -

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Basic information

Entry
Database: PDB / ID: 6x7o
TitleLnmK in complex with 2-sulfonate-propionyl-CoA
ComponentsBifunctional methylmalonyl-CoA:ACP acyltransferase/decarboxylase
Keywordstransferase/transferase inhibitor / transferase / lyase / inhibitor / isostere / transferase-transferase inhibitor complex
Function / homology
Function and homology information


S-acyltransferase activity
Similarity search - Function
: / LnmK, N-terminal / LnmK N-terminal Hot Dog Fold domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
(2R)-sulfonatepropionyl-CoA / (2S)-sulfonatepropionyl-CoA / Conserved hypthetical protein
Similarity search - Component
Biological speciesStreptomyces atroolivaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsStunkard, L.M. / Kick, B.J. / Lohman, J.R.
CitationJournal: Biochemistry / Year: 2021
Title: Structures of LnmK, a Bifunctional Acyltransferase/Decarboxylase, with Substrate Analogues Reveal the Basis for Selectivity and Stereospecificity.
Authors: Stunkard, L.M. / Kick, B.J. / Lohman, J.R.
History
DepositionMay 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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: Bifunctional methylmalonyl-CoA:ACP acyltransferase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5727
Polymers35,3801
Non-polymers2,1926
Water5,260292
1
A: Bifunctional methylmalonyl-CoA:ACP acyltransferase/decarboxylase
hetero molecules

A: Bifunctional methylmalonyl-CoA:ACP acyltransferase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,14414
Polymers70,7612
Non-polymers4,38312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area4970 Å2
ΔGint-127 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.110, 61.110, 312.261
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Bifunctional methylmalonyl-CoA:ACP acyltransferase/decarboxylase


Mass: 35380.387 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atroolivaceus (bacteria) / Gene: LnmK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GGP1
#2: Chemical ChemComp-YXS / (2S)-sulfonatepropionyl-CoA / (2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 903.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O20P3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-YXR / (2R)-sulfonatepropionyl-CoA / (2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]me thoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfany l]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 903.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O20P3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 3% PEG400, 67 mM Bis-Tris pH 6.5, 33 mM Bis-Tris pH 7.5, 28% PEG3350
PH range: 6.5-7.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2016 / Details: MD2 microdifractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 51831 / % possible obs: 99.9 % / Redundancy: 20.3 % / Biso Wilson estimate: 29.64 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.069 / Net I/σ(I): 101.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 17.1 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5079 / Rsym value: 1.23 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZO

4hzo


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.655 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2608 5 %RANDOM
Rwork0.175 ---
obs0.177 49087 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 88 292 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132515
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172254
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.6723443
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5945193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9719.803152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05715374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5531530
X-RAY DIFFRACTIONr_chiral_restr0.2230.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 168 -
Rwork0.286 3545 -
obs--99.95 %

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