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- PDB-8shh: Crystal structure of EvdS6 decarboxylase in ligand free state -

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Basic information

Entry
Database: PDB / ID: 8shh
TitleCrystal structure of EvdS6 decarboxylase in ligand free state
ComponentsdTDP-glucose 4,6-dehydratase
KeywordsLYASE / Decarboxylase / NDP- glucuronic acid
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 14, 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)77,1867
Polymers75,5412
Non-polymers1,6455
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-19 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.783, 77.489, 146.882
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

#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
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein concentration= 9mg/ml, Reservoir solution=0.1M Hepes pH7.0 and 10% w/v [PEG] 6000

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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: 1.92→50 Å / Num. obs: 49037 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.11 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.072 / Net I/σ(I): 27.465
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 2387 / CC1/2: 0.675

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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: 1.93→38.74 Å / SU ML: 0.2339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 2331 4.77 %
Rwork0.1903 46571 -
obs0.1924 48902 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.88 Å2
Refinement stepCycle: LAST / Resolution: 1.93→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 109 264 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695153
X-RAY DIFFRACTIONf_angle_d0.86677040
X-RAY DIFFRACTIONf_chiral_restr0.0522779
X-RAY DIFFRACTIONf_plane_restr0.0076911
X-RAY DIFFRACTIONf_dihedral_angle_d13.26291784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.31191070.29152328X-RAY DIFFRACTION85.32
1.97-2.010.28631250.24722711X-RAY DIFFRACTION99.47
2.01-2.060.27131440.22452707X-RAY DIFFRACTION99.65
2.06-2.110.26291280.21592746X-RAY DIFFRACTION99.86
2.11-2.170.26361290.21392724X-RAY DIFFRACTION99.69
2.17-2.230.28081190.20362764X-RAY DIFFRACTION99.83
2.23-2.310.25391340.20312723X-RAY DIFFRACTION99.83
2.31-2.390.24291420.19472736X-RAY DIFFRACTION99.97
2.39-2.480.2951640.19422731X-RAY DIFFRACTION99.97
2.48-2.60.24561230.19532791X-RAY DIFFRACTION99.97
2.6-2.730.23061320.19112742X-RAY DIFFRACTION99.97
2.73-2.90.24921390.19732754X-RAY DIFFRACTION99.97
2.9-3.130.25861410.19232795X-RAY DIFFRACTION99.97
3.13-3.440.21981520.19482764X-RAY DIFFRACTION99.79
3.44-3.940.23981630.18122771X-RAY DIFFRACTION99.76
3.94-4.960.18941430.16772825X-RAY DIFFRACTION99.83
4.96-38.740.20981460.18052959X-RAY DIFFRACTION98.85

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