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- PDB-7i03: PanDDA analysis group deposition -- Crystal structure of Enteroco... -

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Basic information

Entry
Database: PDB / ID: 7i03
TitlePanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000027858187
ComponentsStreptogramin A acetyltransferase
KeywordsTRANSFERASE / VatD / antibiotic resistance / streptogramin / fragment-based drug discovery
Function / homology
Function and homology information


acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic
Similarity search - Function
: / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
1-benzofuran-2-sulfonamide / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsAsthana, P. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145238 United States
CitationJournal: To be published
Title: Ligand screen against Enterococcus faecium VatD
Authors: Asthana, P. / Fraser, J.S.
History
DepositionJan 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptogramin A acetyltransferase
B: Streptogramin A acetyltransferase
C: Streptogramin A acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0014
Polymers70,8043
Non-polymers1971
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-46 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.930, 102.233, 146.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Streptogramin A acetyltransferase / Virginiamycin acetyltransferase D / Vat(D)


Mass: 23601.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HIS6 purification tag (MGSSHHHHHHENLYFQ) cleaved with TEV protease
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: vatD, satA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P50870, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-EVD / 1-benzofuran-2-sulfonamide


Mass: 197.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM TRIS, 25% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 2.16→48.67 Å / Num. obs: 36113 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.93 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.081 / Rrim(I) all: 0.203 / Net I/σ(I): 10 / Num. measured all: 234543
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.16-2.236.32.9971872929880.1791.2873.270.697
8.91-48.675.90.03436026070.9980.0160.03746.499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
Aimless0.7.9data scaling
PDB_EXTRACT3.28data extraction
XDSJun 30, 2023data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→48.25 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 1818 5.06 %
Rwork0.2226 34137 -
obs0.2257 35955 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.37 Å2 / Biso mean: 64.8244 Å2 / Biso min: 23.19 Å2
Refinement stepCycle: final / Resolution: 2.16→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 20 31 4872
Biso mean--65.39 62.35 -
Num. residues----608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.220.42941340.40382466260095
2.22-2.290.44281340.361926052739100
2.29-2.360.38721350.342825712706100
2.36-2.440.33891450.321926052750100
2.44-2.540.40221480.323725842732100
2.54-2.660.4051230.289426232746100
2.66-2.80.38051190.274626172736100
2.8-2.970.35661430.257526222765100
2.97-3.20.3511450.271226292774100
3.2-3.520.26531430.221726332776100
3.52-4.030.28141460.196426722818100
4.03-5.080.20941440.149326922836100
5.08-48.250.20771590.181228182977100

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