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- PDB-7i0g: PanDDA analysis group deposition -- Crystal structure of Enteroco... -

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Basic information

Entry
Database: PDB / ID: 7i0g
TitlePanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000158650
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
2-HYDROXYMETHYL-BENZOIMIDAZOLE / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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

Downloads & links

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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)70,9524
Polymers70,8043
Non-polymers1481
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-48 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.691, 101.948, 145.045
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-XIY / 2-HYDROXYMETHYL-BENZOIMIDAZOLE / 1H-BENZIMIDAZOL-2-YLMETHANOL


Mass: 148.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
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: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.05→48.35 Å / Num. obs: 41368 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 44.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.053 / Rrim(I) all: 0.135 / Net I/σ(I): 9.5 / Num. measured all: 265969
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.112.3791822731250.2311.0692.6140.799.3
8.96-48.350.03634635930.9990.0160.03939.299.6

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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: 2.05→48.09 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 2074 5.03 %
Rwork0.2165 39197 -
obs0.2193 41271 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.42 Å2 / Biso mean: 61.8982 Å2 / Biso min: 24.48 Å2
Refinement stepCycle: final / Resolution: 2.05→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 19 7 4847
Biso mean--64.24 50.81 -
Num. residues----608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10.45251260.38862556268298
2.1-2.160.4141270.363625482675100
2.16-2.210.36181420.344425752717100
2.21-2.280.35281340.312425802714100
2.28-2.350.37271410.302925902731100
2.35-2.440.33811420.277225842726100
2.44-2.530.32921430.262625832726100
2.53-2.650.32041230.252225922715100
2.65-2.790.31831220.241226022724100
2.79-2.960.32081430.240426092752100
2.96-3.190.31211400.244626282768100
3.19-3.510.28651440.216626052749100
3.51-4.020.26631440.200126622806100
4.02-5.070.20081440.153926742818100
5.07-48.090.21221590.179728092968100

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