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- PDB-5ep5: The crystal structure of the hypothetical protein SAV0944 mutant ... -

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Basic information

Entry
Database: PDB / ID: 5ep5
TitleThe crystal structure of the hypothetical protein SAV0944 mutant (Glu47Ala) from Staphylococcus aureus.
Componentsthioesterase
KeywordsHYDROLASE / Thioesterases / hypothetical protein SAV0944 / staphylococcus aureus / coenzyme A.
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Thioesterase domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
Citation
Journal: TO BE PUBLISHED
Title: The crystal structure of the hypothetical protein SAV0944 mutant (Glu47Ala) from Staphylococcus aureus
Authors: Khandokar, Y.B. / Roman, N. / Smith, K.M. / Srivastava, P. / Forwood, J.K.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Expression, purification, crystallization and preliminary X-ray analysis of the PaaI-like thioesterase SAV0944 from Staphylococcus aureus.
Authors: Khandokar, Y.B. / Roman, N. / Smith, K.M. / Srivastava, P. / Forwood, J.K.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thioesterase
B: thioesterase
C: thioesterase
D: thioesterase


Theoretical massNumber of molelcules
Total (without water)55,3484
Polymers55,3484
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-36 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.220, 91.570, 65.740
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
thioesterase


Mass: 13836.954 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV0944 / Plasmid: pMCSG21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: A0A0H3JUJ1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5M Lithium sulphate, 0.1M HEPES Sodium pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→46 Å / Num. obs: 10339 / % possible obs: 89.7 % / Redundancy: 7.3 % / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.9→46 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.845 / SU B: 21.518 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26284 573 5.5 %RANDOM
Rwork0.2174 ---
obs0.21991 9766 89.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å22.13 Å2
2---1.74 Å2-0 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 0 0 3656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193720
X-RAY DIFFRACTIONr_bond_other_d0.0020.023695
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9515031
X-RAY DIFFRACTIONr_angle_other_deg0.93238525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.51224.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61615674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7791512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024115
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02777
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_it2.3883.9571920
X-RAY DIFFRACTIONr_mcbond_other2.3823.9561919
X-RAY DIFFRACTIONr_mcangle_it4.1035.9272393
X-RAY DIFFRACTIONr_mcangle_other4.1045.9282394
X-RAY DIFFRACTIONr_scbond_it2.5184.4821800
X-RAY DIFFRACTIONr_scbond_other2.5174.4831801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3536.5432639
X-RAY DIFFRACTIONr_long_range_B_refined8.31337.66215129
X-RAY DIFFRACTIONr_long_range_B_other8.31337.66115128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 41 -
Rwork0.353 715 -
obs--88.94 %

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