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

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Basic information

Entry
Database: PDB / ID: 7hzv
TitlePanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000438614
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
N-(1,3,4-thiadiazol-2-yl)benzenesulfonamide / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 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)71,0454
Polymers70,8043
Non-polymers2411
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-48 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.690, 101.735, 145.949
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-W6G / N-(1,3,4-thiadiazol-2-yl)benzenesulfonamide


Mass: 241.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: 2022-20-07
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.28→48.65 Å / Num. obs: 30508 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.074 / Rrim(I) all: 0.191 / Net I/σ(I): 7.9 / Num. measured all: 196654
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
2.28-2.366.62.8941932829250.3191.2093.1420.7100
8.83-48.655.40.04432706100.9970.020.04931.799

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
PDB_EXTRACT3.28data extraction
XDSJun 30, 2023data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→48.03 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1542 5.07 %
Rwork0.2026 28883 -
obs0.2061 30425 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.53 Å2 / Biso mean: 66.9104 Å2 / Biso min: 22.12 Å2
Refinement stepCycle: final / Resolution: 2.28→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 22 20 4863
Biso mean--73.13 60.4 -
Num. residues----608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.350.44151390.39142571271099
2.35-2.440.39621420.351425792721100
2.44-2.540.38691450.35052540268599
2.54-2.650.35171200.290726142734100
2.65-2.790.39831220.25826222744100
2.79-2.970.30791390.238326142753100
2.97-3.190.33511440.244326202764100
3.19-3.520.27121440.19482606275099
3.52-4.020.28391450.180326442789100
4.02-5.070.19761440.14252670281499
5.07-48.030.21121580.16852803296199

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