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- PDB-7i04: PanDDA analysis group deposition -- Crystal structure of Enteroco... -

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Basic information

Entry
Database: PDB / ID: 7i04
TitlePanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000002561227
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
3-(dimethylamino)benzohydrazide / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)70,9834
Polymers70,8043
Non-polymers1791
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-47 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.114, 101.017, 146.440
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
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-47S / 3-(dimethylamino)benzohydrazide


Mass: 179.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
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: 1.11588 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: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.9→48.81 Å / Num. obs: 52285 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 44.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.042 / Rrim(I) all: 0.106 / Net I/σ(I): 8.4 / Num. measured all: 336156
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
1.9-1.946.32.2162066232550.3030.9342.410.597.8
9.11-48.815.90.05633475690.9970.0250.06124.699.4

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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: 1.9→47.75 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 2590 4.98 %
Rwork0.2187 49470 -
obs0.2214 52060 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.21 Å2 / Biso mean: 61.6592 Å2 / Biso min: 19.42 Å2
Refinement stepCycle: final / Resolution: 1.9→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 26 34 4881
Biso mean--60.77 65.7 -
Num. residues----608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.940.46391340.46522391252592
1.94-1.970.44521300.406425622692100
1.97-2.010.3941400.34232569270998
2.01-2.060.3989990.319225872686100
2.06-2.10.32121280.29572575270399
2.1-2.160.33281270.287625832710100
2.16-2.220.35371480.26962570271899
2.22-2.280.32431330.26082556268999
2.28-2.350.33611420.26062596273899
2.35-2.440.31411380.278126072745100
2.44-2.540.34641490.281825602709100
2.54-2.650.32261260.255826252751100
2.65-2.790.32921220.25626252747100
2.79-2.970.29881410.254726332774100
2.97-3.190.33991430.270626362779100
3.19-3.520.26041410.222126322773100
3.52-4.020.25981520.1972658281099
4.02-5.070.19441360.145926882824100
5.07-47.750.21821610.17752817297899

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