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- PDB-1khr: Crystal Structure of Vat(D) in Complex with Virginiamycin and Coe... -

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Basic information

Entry
Database: PDB / ID: 1khr
TitleCrystal Structure of Vat(D) in Complex with Virginiamycin and Coenzyme A
ComponentsSTREPTOGRAMIN A ACETYLTRANSFERASE
Keywordstransferase/antibiotic / Antibiotic resistance / Acyltransferase / transferase-antibiotic complex
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
COENZYME A / VIRGINIAMYCIN M1 / Streptogramin A acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSugantino, M. / Roderick, S.L.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal structure of Vat(D): an acetyltransferase that inactivates streptogramin group A antibiotics.
Authors: Sugantino, M. / Roderick, S.L.
History
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

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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
D: STREPTOGRAMIN A ACETYLTRANSFERASE
E: STREPTOGRAMIN A ACETYLTRANSFERASE
F: STREPTOGRAMIN A ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,23415
Polymers142,0526
Non-polymers6,1829
Water2,018112
1
A: STREPTOGRAMIN A ACETYLTRANSFERASE
B: STREPTOGRAMIN A ACETYLTRANSFERASE
C: STREPTOGRAMIN A ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3808
Polymers71,0263
Non-polymers3,3545
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-55 kcal/mol
Surface area24670 Å2
MethodPISA
2
D: STREPTOGRAMIN A ACETYLTRANSFERASE
E: STREPTOGRAMIN A ACETYLTRANSFERASE
F: STREPTOGRAMIN A ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8547
Polymers71,0263
Non-polymers2,8284
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-49 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.100, 185.900, 186.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
DetailsThe biological unit is a trimer. Chains A, B and C form one trimer. Chains D, E and F form one 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) / Gene: satA / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P50870, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-VIR / VIRGINIAMYCIN M1


Mass: 525.593 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C28H35N3O7 / Comment: antibiotic*YM
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, ethanol, sodium citrate, tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-35 %PEG4001reservoir
25-8 %ethanol1reservoir
30.2 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Oct 5, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 37772 / Num. obs: 37772 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.296 / % possible all: 91.9
Reflection
*PLUS
Redundancy: 3.6 % / Num. measured all: 135079
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 91.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
XDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1863 5.1 %RANDOM
Rwork0.186 ---
all0.189 36450 --
obs0.189 36450 91.4 %-
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.26 Å
Luzzati d res low-6 Å
Luzzati sigma a0.43 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9678 0 402 112 10192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.891.5
X-RAY DIFFRACTIONx_mcangle_it2.662
X-RAY DIFFRACTIONx_scbond_it2.872
X-RAY DIFFRACTIONx_scangle_it4.072.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 266 4.8 %
Rwork0.248 5329 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2COA.PARTOPH19.SOL
X-RAY DIFFRACTION3VIR.PARCOA.TOP
X-RAY DIFFRACTION4VIR.TOP
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75
X-RAY DIFFRACTIONx_mcbond_it1.891.5
X-RAY DIFFRACTIONx_scbond_it2.872
X-RAY DIFFRACTIONx_mcangle_it2.662
X-RAY DIFFRACTIONx_scangle_it4.072.5
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.321 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.248 / Rfactor obs: 0.248

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