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- PDB-1mr9: Crystal structure of Streptogramin A Acetyltransferase with acety... -

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Basic information

Entry
Database: PDB / ID: 1mr9
TitleCrystal structure of Streptogramin A Acetyltransferase with acetyl-CoA bound
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 / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,16012
Polymers144,3036
Non-polymers4,8576
Water00
1
A: Streptogramin A Acetyltransferase
B: Streptogramin A Acetyltransferase
C: Streptogramin A Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5806
Polymers72,1513
Non-polymers2,4293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-38 kcal/mol
Surface area24000 Å2
MethodPISA
2
X: Streptogramin A Acetyltransferase
Y: Streptogramin A Acetyltransferase
Z: Streptogramin A Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5806
Polymers72,1513
Non-polymers2,4293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-35 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.516, 184.530, 186.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41X
51Y
61Z

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1MSEMSEARGARGAA1 - 2031 - 203
2MSEMSEARGARGBB1 - 2031 - 203
3MSEMSEILEILECC1 - 2021 - 202
4MSEMSEARGARGXD1 - 2031 - 203
5GLYGLYILEILEYE2 - 2022 - 202
6GLYGLYILEILEZF2 - 2022 - 202
Detailsbiological trimer

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Components

#1: Protein
Streptogramin A Acetyltransferase


Mass: 24050.486 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: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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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: 2.88 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 2.9M Sodium Formate, 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 14, 2001 / Details: Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 31022 / Redundancy: 2.62 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.07 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.25
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 96.9 % / Redundancy: 3.18 % / Num. measured all: 173203 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 98 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.82

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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: 3→20 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.843 / SU ML: 0.656 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29506 1425 5.1 %RANDOM
Rwork0.24282 ---
all0.24557 ---
obs0.24557 26609 89.73 %-
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: 62.715 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---0.79 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9370 0 302 0 9672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229916
X-RAY DIFFRACTIONr_bond_other_d0.0010.028783
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.98313542
X-RAY DIFFRACTIONr_angle_other_deg1.794320554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.34231202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.784151692
X-RAY DIFFRACTIONr_chiral_restr0.3140.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210835
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021770
X-RAY DIFFRACTIONr_nbd_refined0.2610.33000
X-RAY DIFFRACTIONr_nbd_other0.2390.310763
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.51048
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1240.545
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.378
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.53
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: 2821 / Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A0.61
2B0.6
3C0.64
4X0.62
5Y0.64
6Z0.63
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.366 98
Rwork0.298 2019
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)
11.82282.34780.24134.03020.540.7003-0.06310.0724-0.2659-0.0966-0.0253-0.30120.2762-0.00660.08830.2963-0.04740.05770.2876-0.02440.239327.132253.830614.4805
23.25732.4684-1.95473.2044-0.972.53460.3027-0.29690.33030.4965-0.29750.0120.01040.1535-0.00520.1868-0.1013-0.05280.2431-0.0170.28437.1681.035527.1489
30.89150.1379-0.36931.67561.04012.31150.2634-0.35230.07580.316-0.32580.26890.0534-0.40710.06240.3973-0.27860.11390.4824-0.06580.279813.507565.253240.6256
42.2659-0.15210.28931.5483-0.38560.9577-0.0930.1032-0.207-0.12730.0791-0.1755-0.01890.07780.01390.16770.03940.02770.1455-0.03250.212439.8463107.346266.0048
50.97560.484-0.2412.71921.80612.68490.07640.25760.1211-0.401-0.17260.493-0.1426-0.54840.09620.21080.0746-0.11130.39320.01790.291312.9268119.533255.7098
63.6794-2.3592-0.30823.12190.04240.111-0.0488-0.38540.42320.45710.1349-0.0637-0.0671-0.0076-0.0860.3755-0.01420.03220.2461-0.09950.222826.354131.527480.8784
720.3034-20.9779-0.06256.7312-11.972110.73752.1725-0.0192-0.697-1.7885-0.36450.90923.30810.77-1.80810.2283-0.16970.00760.24070.00030.473840.012464.157321.3837
812.325424.4361-15.3191-3.6962-4.05846.2125-0.33991.35841.28230.5614-0.7129-1.96931.8903-2.07471.05280.2352-0.11520.00520.9047-0.1620.442429.685272.905141.1323
913.637325.2875-17.4595-21.478428.294456.3158-0.3727-2.62820.7052-0.02860.2061-1.3317-0.7824-0.03570.16670.5004-0.2162-0.05110.2898-0.12730.520721.880752.321731.7602
10137.624674.4494-14.236460.1264-8.68548.9669-1.14880.7802-3.4032-1.4787-0.4811-3.02560.00280.13831.62990.17480.0589-0.16710.2488-0.04810.1630.1598114.977653.1954
1144.86974.7294-26.7822-15.749421.032522.39360.2713-0.0648-0.023-1.353-0.2784-0.0838-1.6194-1.34550.00710.55540.11670.22760.3827-0.09050.538720.4626133.619163.3177
1221.261115.5359-2.97388.76232.226415.3683-0.282-0.6065-0.7440.7558-0.1334-1.9144-0.95650.56820.41540.18440.1227-0.01130.1614-0.1240.573740.2149124.281572.782
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 - 2021 - 202
4X-RAY DIFFRACTION4XD1 - 2031 - 203
5X-RAY DIFFRACTION5YE2 - 2022 - 202
6X-RAY DIFFRACTION6ZF2 - 2022 - 202
7X-RAY DIFFRACTION7BG300
8X-RAY DIFFRACTION8BH301
9X-RAY DIFFRACTION9AI302
10X-RAY DIFFRACTION10YJ303
11X-RAY DIFFRACTION11ZK304
12X-RAY DIFFRACTION12XL305
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.63

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