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- PDB-6x7n: LnmK in complex with 2-nitronate-propionyl-amino(dethia)-CoA -

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Basic information

Entry
Database: PDB / ID: 6x7n
TitleLnmK in complex with 2-nitronate-propionyl-amino(dethia)-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
Chem-KGJ / Conserved hypthetical protein
Similarity search - Component
Biological speciesStreptomyces atroolivaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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

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)36,6156
Polymers35,3801
Non-polymers1,2355
Water5,459303
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)73,23012
Polymers70,7612
Non-polymers2,47010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5120 Å2
ΔGint-123 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.875, 60.875, 309.488
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

21A-767-

HOH

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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-KGJ / [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]ethylamino]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium


Mass: 850.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H39N9O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 150 mM ammonium sulfate, 100 mM HEPES pH 7.0, 24% PEG3350, and 15% PEG400
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: Jun 14, 2016 / Details: MD2 microdifractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.42→29.88 Å / Num. obs: 65021 / % possible obs: 99.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 25.631 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Rsym value: 0.076 / Χ2: 1.084 / Net I/av σ(I): 23.838 / Net I/σ(I): 176.4
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 6335 / CC1/2: 0.823 / CC star: 0.95 / Rpim(I) all: 0.327 / Rrim(I) all: 1.081 / Rsym value: 1.001 / Χ2: 1.033 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZO

4hzo


Resolution: 1.42→29.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.37 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 3302 5.1 %RANDOM
Rwork0.1922 ---
obs0.1938 61663 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.65 Å2 / Biso mean: 25.631 Å2 / Biso min: 12.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 1.42→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 53 306 2731
Biso mean--33.76 35.84 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132600
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172340
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.6673565
X-RAY DIFFRACTIONr_angle_other_deg1.5871.5925400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1519.503161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0561533
X-RAY DIFFRACTIONr_chiral_restr0.0930.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023011
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02627
LS refinement shellResolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 222 -
Rwork0.292 4158 -
all-4380 -
obs--92.91 %

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