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- PDB-8sk0: Crystal structure of EvdS6 decarboxylase in ligand bound state -

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Basic information

Entry
Database: PDB / ID: 8sk0
TitleCrystal structure of EvdS6 decarboxylase in ligand bound state
ComponentsdTDP-glucose 4,6-dehydratase
KeywordsLYASE / Decarboxylase / NDP- glucuronic acid / TDP / citrate
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / nucleotide binding
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CITRATE ANION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / THYMIDINE-5'-DIPHOSPHATE / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSharma, P. / Frigo, L. / Dulin, C.C. / Bachmann, B.O. / Iverson, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI140400 United States
American Heart Association19POST34450093 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster.
Authors: Dulin, C.C. / Sharma, P. / Frigo, L. / Voehler, M.W. / Iverson, T.M. / Bachmann, B.O.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dTDP-glucose 4,6-dehydratase
B: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7499
Polymers75,5412
Non-polymers2,2087
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-30 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.984, 76.405, 148.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein dTDP-glucose 4,6-dehydratase / Glucuronic acid decarboxylase


Mass: 37770.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Gene: GA0070563_112236 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1C5ADV9, dTDP-glucose 4,6-dehydratase

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Non-polymers , 6 types, 837 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein concentration= 9mg/ml, Reservoir solution= 2% v/v tacsimate pH 5.0, 100mM sodium citrate tribasic dihydrate pH 5.6, 16% w/v polyethylene glycol [PEG] 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 106406 / % possible obs: 98.9 % / Redundancy: 4 % / Biso Wilson estimate: 14.83 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 25.32
Reflection shellResolution: 1.51→1.54 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5314 / CC1/2: 0.725 / Rsym value: 0.604 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→33.97 Å / SU ML: 0.1482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 5240 4.94 %
Rwork0.173 100833 -
obs0.1743 106073 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.51→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 145 830 6009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00635369
X-RAY DIFFRACTIONf_angle_d0.8897356
X-RAY DIFFRACTIONf_chiral_restr0.0533808
X-RAY DIFFRACTIONf_plane_restr0.0087953
X-RAY DIFFRACTIONf_dihedral_angle_d12.48961893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.25541600.22033189X-RAY DIFFRACTION93.42
1.53-1.550.25391590.21193333X-RAY DIFFRACTION98.84
1.55-1.560.24121800.20113365X-RAY DIFFRACTION99.36
1.56-1.580.24911540.2063343X-RAY DIFFRACTION99.49
1.58-1.60.24051860.20553336X-RAY DIFFRACTION99.32
1.6-1.630.22421590.20333400X-RAY DIFFRACTION99.36
1.63-1.650.23311720.19043327X-RAY DIFFRACTION99.35
1.65-1.670.21881800.18923386X-RAY DIFFRACTION99.3
1.67-1.70.23671730.17843346X-RAY DIFFRACTION99.49
1.7-1.730.20621680.18543356X-RAY DIFFRACTION99.38
1.73-1.760.21981640.19183385X-RAY DIFFRACTION99.47
1.76-1.790.23541710.19223348X-RAY DIFFRACTION99.58
1.79-1.820.2281680.18663414X-RAY DIFFRACTION99.39
1.83-1.860.19721800.19223350X-RAY DIFFRACTION99.16
1.86-1.90.2181750.19773349X-RAY DIFFRACTION99.24
1.9-1.950.2761520.21793357X-RAY DIFFRACTION98.18
1.95-20.23611720.19223368X-RAY DIFFRACTION99.1
2-2.050.22181890.18873330X-RAY DIFFRACTION98.74
2.05-2.110.20941710.18423345X-RAY DIFFRACTION98.35
2.11-2.180.19751930.18483318X-RAY DIFFRACTION98.29
2.18-2.260.20561700.18613224X-RAY DIFFRACTION93.99
2.26-2.350.20721570.18613177X-RAY DIFFRACTION93.42
2.35-2.450.22351810.17433400X-RAY DIFFRACTION98.9
2.45-2.580.20351970.17343360X-RAY DIFFRACTION99.16
2.58-2.740.19051890.17273434X-RAY DIFFRACTION99.67
2.74-2.960.19621780.17373440X-RAY DIFFRACTION99.81
2.96-3.250.20521760.16543455X-RAY DIFFRACTION99.84
3.25-3.720.18781920.15553383X-RAY DIFFRACTION97.41
3.72-4.690.13581750.13063409X-RAY DIFFRACTION96.97
4.69-33.970.15371990.14373606X-RAY DIFFRACTION98.04

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