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- PDB-1mrl: Crystal structure of streptogramin A acetyltransferase with dalfo... -

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Basic information

Entry
Database: PDB / ID: 1mrl
TitleCrystal structure of streptogramin A acetyltransferase with dalfopristin
ComponentsStreptogramin A acetyltransferase
KeywordsTRANSFERASE / left-handed parallel beta-helix domain
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
Chem-DOL / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKehoe, L.E. / Snidwongse, J. / Courvalin, P. / Rafferty, J.B. / Murray, I.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural Basis of Synercid (Quinupristin-Dalfopristin) Resistance in Gram-positive Bacterial Pathogens
Authors: Kehoe, L.E. / Snidwongse, J. / Courvalin, P. / Rafferty, J.B. / Murray, I.A.
History
DepositionSep 18, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0996
Polymers71,0263
Non-polymers2,0733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-56 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.914, 90.905, 104.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 1 - 204 / Label seq-ID: 1 - 204

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsBiological trimer

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Components

#1: Protein Streptogramin A acetyltransferase


Mass: 23675.326 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
References: UniProt: P50870, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-DOL / 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE / DALFOPRISTIN


Mass: 690.847 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H50N4O9S / Comment: antibiotic*YM

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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: 2.86 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium Fluoride, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.25 mMenzyme1drop
21.5 mMdalfopristin1drop
30.2 Msodium fluoride1reservoir
420 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2002 / Details: Mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 20118 / Redundancy: 3.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.6
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 99.7 % / Num. measured all: 222509
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 99.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MR7

1mr7


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.856 / SU ML: 0.34 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.844 / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30379 1009 5.1 %RANDOM
Rwork0.27063 ---
all0.2723 ---
obs0.2723 18853 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2--2.27 Å20 Å2
3----3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 0 144 0 4888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0225047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9796908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2873625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.40715860
X-RAY DIFFRACTIONr_chiral_restr0.080.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.32158
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.5254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3930.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4330.51
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1543 / Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A0.36
2B0.34
3C0.41
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 76
Rwork0.308 1329
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)
11.8975-2.19220.22224.7596-0.56062.1421-0.4449-0.70460.0760.82520.5413-0.0866-0.03620.244-0.09640.23820.11510.01210.3488-0.02430.122127.750133.464365.5537
21.4222-1.5213-0.36252.95320.91582.96080.17310.19680.1998-0.3552-0.0968-0.0788-0.430.0593-0.07620.14850.00390.03910.08540.06160.149720.596846.150736.8565
31.839-1.12840.03932.39950.40354.29210.01210.0638-0.2287-0.1546-0.0204-0.06490.37930.32530.00830.11070.09760.01610.08620.00860.202133.578716.776738.4944
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2041 - 204
2X-RAY DIFFRACTION2BB1 - 2041 - 204
3X-RAY DIFFRACTION3CC1 - 2041 - 204
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.272
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.003
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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