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

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Basic information

Entry
Database: PDB / ID: 4hur
TitleCrystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with acetyl coenzyme A
ComponentsVirginiamycin A acetyltransferase
KeywordsTRANSFERASE / 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
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
ACETYL COENZYME *A / Virginiamycin A acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Other
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Dec 24, 2014Group: Database references
Revision 1.4Sep 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 / 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)79,57439
Polymers75,0533
Non-polymers4,52136
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17250 Å2
ΔGint-59 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.910, 184.545, 98.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 , 6 types, 654 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 56.49 %
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, 10 mM AcCoA, 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: 2.02→30 Å / Num. obs: 54946 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5 % / Rsym value: 0.091 / Net I/σ(I): 19
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.13 / Num. unique all: 2567 / Rsym value: 0.507 / % possible all: 94

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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: 2.15→29.185 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 1677 3.64 %random
Rwork0.1666 ---
obs0.168 46063 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 280 618 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125497
X-RAY DIFFRACTIONf_angle_d1.3827424
X-RAY DIFFRACTIONf_dihedral_angle_d12.9632090
X-RAY DIFFRACTIONf_chiral_restr0.075784
X-RAY DIFFRACTIONf_plane_restr0.005926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21320.29531330.22643524X-RAY DIFFRACTION95
2.2132-2.28470.28731360.20993604X-RAY DIFFRACTION98
2.2847-2.36630.29111390.19593671X-RAY DIFFRACTION99
2.3663-2.4610.23871410.19013723X-RAY DIFFRACTION100
2.461-2.57290.24951400.19063682X-RAY DIFFRACTION100
2.5729-2.70850.23451400.17823708X-RAY DIFFRACTION100
2.7085-2.8780.23721400.17573711X-RAY DIFFRACTION100
2.878-3.10.19361400.17723717X-RAY DIFFRACTION99
3.1-3.41150.19391410.16323729X-RAY DIFFRACTION100
3.4115-3.90420.16421400.13913709X-RAY DIFFRACTION99
3.9042-4.91510.16241420.12833762X-RAY DIFFRACTION99
4.9151-29.18810.18191450.17853846X-RAY DIFFRACTION98
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)
14.5795-2.4837-0.01672.4487-1.44694.25380.0325-0.23560.06560.42250.0128-0.4585-0.3670.3377-0.07370.2594-0.0823-0.0110.2903-0.02020.2651-12.6385-22.5018-6.74
27.1341-1.4733-2.21483.2414-1.29264.613-0.4078-0.93230.40431.19780.47530.00310.09380.2733-0.10750.8360.1621-0.01760.3695-0.07650.3677-19.35656.9032-13.098
30.99460.5565-0.78375.3395-2.58493.3550.0598-0.15990.02860.49410.15950.5122-0.2382-0.2604-0.2110.19910.01490.05270.28170.01970.257-28.5325-30.4534-6.0608
43.63631.163-3.20523.5702-2.057.5189-0.0333-0.0578-0.1272-0.143-0.1261-0.23820.17490.35480.15720.11040.027-0.04120.2134-0.01710.2339-10.503-32.2399-38.5074
56.42910.73292.03495.99030.81767.308-0.12080.2142-0.3579-0.26810.2025-0.24910.61790.2526-0.08610.31620.02240.10040.23910.04380.2679-18.0466-42.183-9.8986
60.8128-0.15770.54973.0190.554.58460.0960.1839-0.1146-0.5545-0.00930.36060.061-0.457-0.0440.2419-0.0102-0.0980.29970.00650.3094-25.9635-30.3798-46.5894
74.34331.84052.31586.54073.61287.1279-0.00640.05290.14840.13290.1611-0.3312-0.3540.4155-0.14810.2459-0.00010.01890.23150.03390.2342-11.3478-0.0204-30.8932
87.7551-0.1127-0.67177.3391-0.25955.2311-0.20130.47640.1315-0.42870.08210.0578-0.16680.12520.11060.384-0.0234-0.05030.2880.00010.1826-16.6053-20.1314-54.1718
92.0272-0.18250.21975.70541.54173.2679-0.0754-0.0870.39410.26790.02740.56-0.6969-0.32250.07360.41150.13030.03990.30940.04550.3498-27.76334.729-26.4355
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 7:84
5X-RAY DIFFRACTION5chain B and resi 85:113
6X-RAY DIFFRACTION6chain B and resi 114:216
7X-RAY DIFFRACTION7chain C and resi 6:84
8X-RAY DIFFRACTION8chain C and resi 85:113
9X-RAY DIFFRACTION9chain C and resi 114:215

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