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

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Basic information

Entry
Database: PDB / ID: 4myo
TitleCrystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus
ComponentsVirginiamycin A acetyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / ANTIBIOTIC RESISTANCE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / LEFT-HANDED BETA HELIX DOMAIN / XENOBIOTIC ACYLTRANSFERASE (XAT) FAMILY / HEXAPEPTIDE REPEAT ACYLTRANSFERASE / STREPTOGRAMIN GROUP A ANTIBIOTICS / STREPTOGRAMIN A / VIRGINIAMYCIN / 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 / 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
Virginiamycin A acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.696 Å
AuthorsStogios, P.J. / Minasov, G. / Dong, A. / Evdokimova, E. / 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
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 16, 2013ID: 4E8L
Revision 1.0Oct 16, 2013Provider: 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 / 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)73,65018
Polymers72,9483
Non-polymers70215
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-164 kcal/mol
Surface area28840 Å2
MethodPISA
2
A: Virginiamycin A acetyltransferase
B: Virginiamycin A acetyltransferase
C: Virginiamycin A acetyltransferase
hetero molecules

A: Virginiamycin A acetyltransferase
B: Virginiamycin A acetyltransferase
C: Virginiamycin A acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,30136
Polymers145,8966
Non-polymers1,40530
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area21590 Å2
ΔGint-338 kcal/mol
Surface area55970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.836, 184.037, 96.909
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-429-

HOH

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Components

#1: Protein Virginiamycin A acetyltransferase


Mass: 24315.986 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M POTASSIUM/SODIUM TARTRATE, 2 M AMMONIUM SULFATE, 0.1 M TRI-SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 7, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.696→25 Å / Num. obs: 22987 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.1 % / Rsym value: 0.078 / Net I/σ(I): 10.74
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.013 / Rsym value: 0.368 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MR7

1mr7


Resolution: 2.696→24.666 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 1148 5 %
Rwork0.1896 --
obs0.1928 22953 99.71 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.696→24.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 27 115 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035234
X-RAY DIFFRACTIONf_angle_d0.6917084
X-RAY DIFFRACTIONf_dihedral_angle_d10.7741963
X-RAY DIFFRACTIONf_chiral_restr0.048751
X-RAY DIFFRACTIONf_plane_restr0.003911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6964-2.8190.31111390.24922635X-RAY DIFFRACTION98
2.819-2.96740.33721420.25282720X-RAY DIFFRACTION100
2.9674-3.15290.30981420.23552686X-RAY DIFFRACTION100
3.1529-3.39580.27541420.22742685X-RAY DIFFRACTION100
3.3958-3.73650.26451430.18312722X-RAY DIFFRACTION100
3.7365-4.27470.23141430.16072741X-RAY DIFFRACTION100
4.2747-5.37650.2091460.14612758X-RAY DIFFRACTION100
5.3765-24.66680.22951510.18532858X-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)
16.1609-0.77354.31815.6068-2.26938.7297-0.02430.05790.30030.09720.1651-0.4574-0.08750.2966-0.10620.38430.02230.05330.1926-0.06470.3184-10.464231.8536-11.2982
25.9531-4.5009-0.16888.66253.47884.2519-0.3524-0.04380.76350.08320.4372-0.7806-0.41740.2271-0.13960.55780.0010.00170.29290.06840.3786-18.001741.8553-39.5095
31.95230.19140.43013.13241.00153.6543-0.0757-0.36890.22010.64340.05290.2094-0.3529-0.58980.02610.53090.10170.08080.35440.02630.3107-26.313330.3033-3.1688
46.85111.92110.58085.9723-0.3186.82540.07030.3318-0.2671-0.41360.0257-0.48940.54710.4579-0.0860.35380.09730.02790.2720.03840.365-12.123322.362-42.811
55.24342.12041.48120.89851.14286.5054-0.10780.67280.1587-0.09520.18760.2385-0.46020.3559-0.11120.7796-0.0609-0.0570.41120.00260.3136-18.8566-7.3249-36.6874
61.7143-0.73490.28247.1201-3.94084.2309-0.00560.21170.0565-0.56230.13570.4842-0.1524-0.3354-0.12350.39040.0203-0.07280.27320.01570.2729-28.156230.3788-43.9193
75.7888-1.7893-3.69045.00311.82446.038-0.0391-0.26430.08540.48360.2102-0.47780.19830.3392-0.17240.4620.0152-0.10610.2410.02450.2748-11.41390.0014-18.5673
82.55723.6377-2.90585.5047-4.31393.4599-0.38180.1032-0.9472-0.19950.1188-0.52110.4144-0.02170.2520.82110.11620.04060.3479-0.03750.4378-16.96119.96644.3221
92.642-0.42170.00546.8131.55062.82510.0450.1136-0.35130.00720.12560.56940.9534-0.3076-0.12030.5523-0.1088-0.06230.35090.06770.3505-27.7217-5.4671-23.5795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 6:84
2X-RAY DIFFRACTION2chain A and resid 85:113
3X-RAY DIFFRACTION3chain A and resid 114:216
4X-RAY DIFFRACTION4chain B and resid 6:84
5X-RAY DIFFRACTION5chain B and resid 85:113
6X-RAY DIFFRACTION6chain B and resid 114:217
7X-RAY DIFFRACTION7chain C and resid 7:84
8X-RAY DIFFRACTION8chain C and resid 85:113
9X-RAY DIFFRACTION9chain C and resid 114:217

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