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- PDB-4qlo: Crystal Structure of homoserine o-acetyltransferase from Staphylo... -

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Basic information

Entry
Database: PDB / ID: 4qlo
TitleCrystal Structure of homoserine o-acetyltransferase from Staphylococcus aureus
Componentshomoserine O-acetyltransferase
KeywordsTRANSFERASE / Rossmann Fold / Acetyltransferase / AcetylCo-A Binding
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsThangavelu, B. / Pavlovsky, A.G. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of homoserine O-acetyltransferase from Staphylococcus aureus: the first Gram-positive ortholog structure.
Authors: Thangavelu, B. / Pavlovsky, A.G. / Viola, R.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: homoserine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,2441
Polymers41,2441
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: homoserine O-acetyltransferase

A: homoserine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)82,4892
Polymers82,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3100 Å2
ΔGint-22 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.155, 49.155, 481.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein homoserine O-acetyltransferase


Mass: 41244.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: TCH1516 / Gene: AZ30_00060, metX, SACOL0012, USA300HOU_0012 / Plasmid: pDEST42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8YYT5, homoserine O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.7 M Ammonium formate, 100 mM Imidazole hydrochloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2014
Details: HORIZONTALLY AND VERTICALLY FOCUSING BIMORPH MIRRORS IN KIRKPATRICK-BAEZ CONFIGURATION
RadiationMonochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 83432 / Num. obs: 12887 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.153
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
CrystalCleardata collection
BALBESphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.646 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.853 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29086 635 5 %RANDOM
Rwork0.23988 ---
obs0.24225 12155 91.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.875 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å21.11 Å20 Å2
2--2.23 Å20 Å2
3----7.23 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 0 28 2680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192733
X-RAY DIFFRACTIONr_bond_other_d0.0010.022529
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9383708
X-RAY DIFFRACTIONr_angle_other_deg0.79635790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57323.425146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40115438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4851519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9155.6051309
X-RAY DIFFRACTIONr_mcbond_other2.9145.6021308
X-RAY DIFFRACTIONr_mcangle_it4.4838.3991635
X-RAY DIFFRACTIONr_mcangle_other4.4258.7361636
X-RAY DIFFRACTIONr_scbond_it3.0616.0611424
X-RAY DIFFRACTIONr_scbond_other3.0426.2431425
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8219.2442073
X-RAY DIFFRACTIONr_long_range_B_refined6.88247.9433122
X-RAY DIFFRACTIONr_long_range_B_other6.87847.9543122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.451→2.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 30 -
Rwork0.356 561 -
obs--60.68 %

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