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- PDB-1mr7: Crystal Structure of Streptogramin A Acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 1mr7
TitleCrystal Structure of Streptogramin A Acetyltransferase
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
Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptogramin A Acetyltransferase
B: Streptogramin A Acetyltransferase
C: Streptogramin A Acetyltransferase
X: Streptogramin A Acetyltransferase
Y: Streptogramin A Acetyltransferase
Z: Streptogramin A Acetyltransferase


Theoretical massNumber of molelcules
Total (without water)142,0526
Polymers142,0526
Non-polymers00
Water12,502694
1
A: Streptogramin A Acetyltransferase
B: Streptogramin A Acetyltransferase
C: Streptogramin A Acetyltransferase


Theoretical massNumber of molelcules
Total (without water)71,0263
Polymers71,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-51 kcal/mol
Surface area25140 Å2
MethodPISA
2
X: Streptogramin A Acetyltransferase
Y: Streptogramin A Acetyltransferase
Z: Streptogramin A Acetyltransferase


Theoretical massNumber of molelcules
Total (without water)71,0263
Polymers71,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-51 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.393, 183.001, 184.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
DetailsBiological trimer

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Components

#1: Protein
Streptogramin A Acetyltransferase


Mass: 23675.326 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: P50870, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6553.15
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2901vapor diffusion, hanging dropSodium Formate 2.7M, VAPOR DIFFUSION, HANGING DROP, temperature 290K
2902vapor diffusion, hanging dropSodium Formate 2.7M, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.15-0.25 mMprotein1reservoir
21 mMTris-HCl1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.97947, 0.97939, 0.96863
SYNCHROTRONSRS PX14.220.978
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDNov 10, 2000Mirrors
ADSC QUANTUM 42CCDApr 10, 2001Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 channelMADMx-ray1
2Si 111 channelSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
20.979391
30.968631
40.9781
ReflectionResolution: 1.8→20 Å / Num. obs: 140296 / Redundancy: 3.37 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21.3
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.27
Reflection
*PLUS
% possible obs: 97.2 % / Num. measured all: 1293725
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 91.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→21.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.27 / SU ML: 3.27 / SU Rfree: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20687 6864 5 %RANDOM
Rwork0.17636 ---
all0.17792 ---
obs0.17792 129459 97.26 %-
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: 17.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9523 0 0 694 10217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229864
X-RAY DIFFRACTIONr_bond_other_d00.028854
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9513458
X-RAY DIFFRACTIONr_angle_other_deg0.744320779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.04831258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.394151836
X-RAY DIFFRACTIONr_chiral_restr0.1080.21452
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210960
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021762
X-RAY DIFFRACTIONr_nbd_refined0.2240.32256
X-RAY DIFFRACTIONr_nbd_other0.2030.39377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.51614
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2360.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.390
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.521
X-RAY DIFFRACTIONr_mcbond_it3.3041.56115
X-RAY DIFFRACTIONr_mcangle_it4.60129983
X-RAY DIFFRACTIONr_scbond_it6.80433749
X-RAY DIFFRACTIONr_scangle_it8.6084.53475
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 481
Rwork0.225 8928
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)
11.41321.4618-0.01242.01790.07410.5504-0.02060.1261-0.1705-0.05610.0522-0.20550.0842-0.0493-0.03160.0749-0.00640.01290.0758-0.01940.106626.978853.163114.0334
21.68270.6552-1.22530.8886-0.39771.310.08-0.10670.04670.0849-0.057-0.0682-0.07860.0596-0.0230.0381-0.0408-0.0310.0742-0.01560.10337.068880.213326.7964
30.5880.036-0.10191.66281.23831.64650.0606-0.089-0.00640.1983-0.10960.10730.0876-0.16140.04890.112-0.06880.01720.13820.01630.059213.30764.374940.2023
41.35960.0570.70790.8852-0.13751.0418-0.00170.0965-0.1022-0.0594-0.0068-0.11450.03920.09190.00850.02980.02070.01780.0555-0.01990.084739.8099106.388564.851
50.68190.2165-0.05131.32531.02321.837-0.00710.0438-0.0017-0.1516-0.08050.1637-0.0653-0.22110.08760.08180.0387-0.04670.1205-0.0010.057112.6726118.399554.7057
61.8401-1.3638-0.31761.75690.2230.34980.0082-0.230.10870.1540.0309-0.0615-0.0548-0.0195-0.03920.1088-0.0273-0.01870.0979-0.03720.06226.4672130.248280.1376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2031 - 203
2X-RAY DIFFRACTION2BB1 - 2031 - 203
3X-RAY DIFFRACTION3CC1 - 2031 - 203
4X-RAY DIFFRACTION4XD1 - 2031 - 203
5X-RAY DIFFRACTION5YE1 - 2031 - 203
6X-RAY DIFFRACTION6ZF1 - 2031 - 203
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.24

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