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- PDB-3dho: Structure of Streptogramin Acetyltransferase in Complex with an I... -

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Basic information

Entry
Database: PDB / ID: 3dho
TitleStructure of Streptogramin Acetyltransferase in Complex with an Inhibitor
ComponentsStreptogramin A acetyltransferase
KeywordsTRANSFERASE / Streptogramin Acetyltransferase Left-Handed Parallel Beta Helix / Acyltransferase / Antibiotic resistance
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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Chem-B2M / FORMIC ACID / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRoderick, S.L. / Pesaresi, A. / Wright, G.D.
CitationJournal: To be Published
Title: Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor
Authors: Johnston, N.J. / Blanchard, J.E. / Koteva, K.P. / Ejim, L.J. / Pesaresi, A. / Roderick, S.L. / Wright, G.D.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Streptogramin A acetyltransferase
E: Streptogramin A acetyltransferase
F: Streptogramin A acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,65427
Polymers142,0526
Non-polymers3,60221
Water24,3201350
1
A: Streptogramin A acetyltransferase
B: Streptogramin A acetyltransferase
C: Streptogramin A acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,00616
Polymers71,0263
Non-polymers1,98013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-44 kcal/mol
Surface area25340 Å2
MethodPISA
2
D: Streptogramin A acetyltransferase
E: Streptogramin A acetyltransferase
F: Streptogramin A acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,64811
Polymers71,0263
Non-polymers1,6228
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-49 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.653, 183.620, 183.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 23675.326 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: vatD, satA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P50870, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-B2M / 6-bromo-N'-[(1Z)-(3,5-dichloro-2-hydroxyphenyl)methylidene]-2-methylquinoline-4-carbohydrazide


Mass: 453.117 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H12BrCl2N3O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1350 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, TEA, Mg-formate, DMSO, inhibitor, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2006
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25.47 Å / Num. obs: 141725 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.9 / Num. unique all: 19437 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CTRdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHR

1khr


Resolution: 1.8→25.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.163 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21318 7132 5 %RANDOM
Rwork0.17597 ---
all0.17785 134570 --
obs0.17785 134570 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.113 Å0.114 Å
Refinement stepCycle: LAST / Resolution: 1.8→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9654 0 207 1350 11211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.97813671
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92751212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.18526.216444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.671151764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6691518
X-RAY DIFFRACTIONr_chiral_restr0.1060.21446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.25409
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26945
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2160
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9251.56226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41429840
X-RAY DIFFRACTIONr_scbond_it2.20234727
X-RAY DIFFRACTIONr_scangle_it3.4074.53831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 523 -
Rwork0.24 9654 -
obs--97.85 %

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