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- PDB-4hus: Crystal structure of streptogramin group A antibiotic acetyltrans... -

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Basic information

Entry
Database: PDB / ID: 4hus
TitleCrystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with virginiamycin M1
ComponentsVirginiamycin A acetyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / STRUCTURAL GENOMICS / ANTIBIOTIC RESISTANCE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / XENOBIOTIC ACYLTRANSFERASE (XAT) FAMILY / HEXAPEPTIDE REPEAT ACYLTRANSFERASE / streptogramin group A antibiotic acetyltransferase / STREPTOGRAMIN GROUP A ANTIBIOTICS / STREPTOGRAMIN A / VIRGINIAMYCIN M1 / DALFOPRISTIN / ACETYL COENZYME A / COENZYME A / INTRACELLULAR / TRANSFERASE-ANTIBIOTIC complex
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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / VIRGINIAMYCIN M1 / Virginiamycin A acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsStogios, P.J. / Minasov, G. / Evdokimova, E. / Wawrzak, Z. / Yim, V. / Krishnamoorthy, M. / Di Leo, R. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: Potential for Reduction of Streptogramin A Resistance Revealed by Structural Analysis of Acetyltransferase VatA.
Authors: Stogios, P.J. / Kuhn, M.L. / Evdokimova, E. / Courvalin, P. / Anderson, W.F. / Savchenko, A.
History
DepositionNov 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Virginiamycin A acetyltransferase
B: Virginiamycin A acetyltransferase
C: Virginiamycin A acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,34543
Polymers75,0533
Non-polymers3,29240
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15920 Å2
ΔGint-160 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.308, 184.735, 98.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-306-

EDO

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Virginiamycin A acetyltransferase


Mass: 25017.736 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: BM3093 / Gene: vat / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P26839, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 8 types, 548 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-VIR / VIRGINIAMYCIN M1


Mass: 525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N3O7 / Comment: antibiotic*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulphate, 0.1 M HEPES pH 7.5, 2% PEG 400, virginiamycin M1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 37898 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6 % / Rsym value: 0.079 / Net I/σ(I): 25.68
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.64 / Rsym value: 0.576 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E8L

4e8l
PDB Unreleased entry


Resolution: 2.36→29.389 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 1751 5 %
Rwork0.1842 --
obs0.1865 34991 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→29.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 196 508 5798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115385
X-RAY DIFFRACTIONf_angle_d1.2387246
X-RAY DIFFRACTIONf_dihedral_angle_d15.6642056
X-RAY DIFFRACTIONf_chiral_restr0.075752
X-RAY DIFFRACTIONf_plane_restr0.004915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.42380.25661350.21932578X-RAY DIFFRACTION100
2.4238-2.49510.28031340.21332526X-RAY DIFFRACTION100
2.4951-2.57560.32091340.21672551X-RAY DIFFRACTION100
2.5756-2.66760.23571360.19872581X-RAY DIFFRACTION100
2.6676-2.77430.25971340.19432535X-RAY DIFFRACTION100
2.7743-2.90050.2631350.2062582X-RAY DIFFRACTION100
2.9005-3.05320.26031350.19632563X-RAY DIFFRACTION100
3.0532-3.24430.25241370.20432576X-RAY DIFFRACTION100
3.2443-3.49440.22761350.18522576X-RAY DIFFRACTION100
3.4944-3.84540.27461180.19752245X-RAY DIFFRACTION87
3.8454-4.40020.15951350.14252564X-RAY DIFFRACTION99
4.4002-5.53780.1851400.14642631X-RAY DIFFRACTION100
5.5378-29.3910.21531430.19562732X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4369-1.2842.86743.7909-2.20887.4844-0.10830.05930.0050.25340.0405-0.1249-0.220.28440.07470.1937-0.00530.07660.23760.00980.215635.961732.1672-11.0927
29.547-0.2842-0.31564.84073.35633.0155-0.189-0.07720.21650.1770.2344-0.2685-0.1652-0.0227-0.03890.40450.0162-0.09960.27510.05070.250428.478842.2349-39.6498
31.17980.192-0.31362.80370.49933.27830.0043-0.24360.01080.55610.02110.48820.0577-0.53880.03340.31980.05070.15450.38690.08090.425320.176530.4968-3.0655
45.30231.7552-0.43698.9644-1.18244.86290.05140.27-0.4943-0.47230.0354-0.20490.39830.4021-0.09360.19680.0827-0.03040.3603-0.0730.313934.346722.8751-42.9345
52.15460.94781.490.6787-0.45845.6186-0.31390.94170.1837-0.85170.33320.3461-0.22580.0546-0.00460.8978-0.1723-0.10960.48950.02440.778227.666-7.1216-36.423
62.0678-0.85970.7024.6127-2.44052.75150.11780.1959-0.4161-0.38780.08010.53370.1582-0.3215-0.19110.2603-0.0015-0.08440.3222-0.05910.371718.379430.5519-43.6725
73.8345-2.2206-2.70965.05863.93598.3085-0.0936-0.077-0.27450.12960.0892-0.08620.52870.3846-0.01510.338-0.0085-0.01380.22750.07440.410135.2260.2093-18.5098
83.8745-0.19491.0213.24321.69531.40340.0947-0.2546-0.18530.41560.01080.20410.41550.0009-0.09920.62810.01810.10080.39880.09070.354429.6820.23984.7061
92.1030.6514-0.38344.09691.05532.5875-0.13020.229-0.45640.0109-0.02840.80250.7188-0.39880.15440.5354-0.1588-0.01750.38410.05350.673918.8895-4.8073-23.3667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 7:84
2X-RAY DIFFRACTION2chain A and resi 85:113
3X-RAY DIFFRACTION3chain A and resi 114:216
4X-RAY DIFFRACTION4chain B and resi 6:84
5X-RAY DIFFRACTION5chain B and resi 85:113
6X-RAY DIFFRACTION6chain B and resi 114:216
7X-RAY DIFFRACTION7chain C and resi 7:84
8X-RAY DIFFRACTION8chain C and resi 85:113
9X-RAY DIFFRACTION9chain C and resi 114:215

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