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- PDB-7i0i: PanDDA analysis group deposition -- Crystal structure of Enteroco... -

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Basic information

Entry
Database: PDB / ID: 7i0i
TitlePanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000001698894
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-hydroxy-2-methylbenzoic acid / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 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)70,9564
Polymers70,8043
Non-polymers1521
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-48 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.640, 101.426, 144.228
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-PF0 / 3-hydroxy-2-methylbenzoic acid


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
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: 1.11581 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: 1.11581 Å / Relative weight: 1
ReflectionResolution: 1.88→48.08 Å / Num. obs: 52775 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Net I/σ(I): 12.3 / Num. measured all: 339667
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
1.88-1.936.22.42055633040.2891.0332.6180.798.8
9.03-48.085.90.02533615720.9990.0110.02850.299.6

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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: 1.88→47.84 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 2613 4.96 %
Rwork0.2245 50033 -
obs0.2269 52646 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.17 Å2 / Biso mean: 54.2769 Å2 / Biso min: 17.19 Å2
Refinement stepCycle: final / Resolution: 1.88→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 18 23 4862
Biso mean--62.03 50.39 -
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 (%)
1.88-1.920.53231380.47582479261797
1.92-1.960.46831370.398125882725100
1.96-1.990.38561260.364226532779100
1.99-2.040.33151110.331125972708100
2.04-2.090.33181320.298926172749100
2.09-2.140.34031270.28925902717100
2.14-2.20.34961450.285226232768100
2.2-2.260.32721330.271226062739100
2.26-2.330.34071380.270926022740100
2.33-2.420.31911420.266226312773100
2.42-2.510.34171490.274425962745100
2.51-2.630.32111280.252326492777100
2.63-2.770.3211170.247226442761100
2.77-2.940.27681470.242126342781100
2.94-3.170.32161480.259826312779100
3.17-3.490.27651430.2226542797100
3.49-3.990.251460.193726872833100
3.99-5.030.19731460.154927082854100
5.03-47.840.21281600.184528443004100

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