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- PDB-6x7l: LnmK in complex with 2-nitronate-propionyl-CoA -

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Basic information

Entry
Database: PDB / ID: 6x7l
TitleLnmK in complex with 2-nitronate-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
ALANINE / Chem-KFV / Conserved hypthetical protein
Similarity search - Component
Biological speciesStreptomyces atroolivaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,9139
Polymers35,3801
Non-polymers1,5338
Water5,621312
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)73,82718
Polymers70,7612
Non-polymers3,06616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5820 Å2
ΔGint-175 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.975, 60.975, 310.859
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-KFV / [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-propan-2-ylidene]-bis(oxidanidyl)azanium


Mass: 867.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38N8O19P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.32 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 150 mM lithium sulfate, 100 mM Bis-Tris pH 7.0, 28% PEG 3350
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-F / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2016 / Details: MD2 microdifractometer
Diffraction measurementDetails: 1.00 degrees, -1.0 sec, detector distance 180.26 mm
Method: \w scans
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionAv R equivalents: 0.079 / Number: 709330
ReflectionResolution: 1.77→30 Å / Num. obs: 34783 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Rsym value: 0.079 / Χ2: 1.035 / Net I/av σ(I): 38.674 / Net I/σ(I): 11.1 / Num. measured all: 709330
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 14.583 / Num. unique obs: 3310 / Rsym value: 0.257 / % possible all: 98.3
Cell measurementReflection used: 709330

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZO

4hzo


Resolution: 1.77→29.94 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.141 / SU ML: 0.069 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1706 4.9 %RANDOM
Rwork0.1639 ---
obs0.1657 32959 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.75 Å2 / Biso mean: 23.525 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----2.41 Å2
Refinement stepCycle: final / Resolution: 1.77→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 68 312 2759
Biso mean--40.01 33.53 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132617
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172367
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6663584
X-RAY DIFFRACTIONr_angle_other_deg1.6661.5945450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7495331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62919.264163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02215399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7821535
X-RAY DIFFRACTIONr_chiral_restr0.0880.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
LS refinement shellResolution: 1.771→1.817 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 123 -
Rwork0.177 2297 -
all-2420 -
obs--97.74 %

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