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- PDB-6fdg: Novel crystal structure of DHNA-CoA Thioesterase from Staphylococ... -

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Basic information

Entry
Database: PDB / ID: 6fdg
TitleNovel crystal structure of DHNA-CoA Thioesterase from Staphylococcus aureus
Components4-hydroxybenzoyl-CoA thioesterase
KeywordsHYDROLASE / THIOESTERASE / Vitamin K2 metabolic pathway
Function / homologyAcyl-CoA thioester hydrolase YbgC/YbaW family / thiolester hydrolase activity / : / Thioesterase domain / Thioesterase superfamily / HotDog domain superfamily / 4-hydroxybenzoyl-CoA thioesterase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsMurad, A.M. / Betzel, C. / Wrenger, C.
Funding support Brazil, 3items
OrganizationGrant numberCountry
FAPESP2013/10288-1 Brazil
FAPESP2012/12790-3 Brazil
CAPESBEX 7454139 Brazil
CitationJournal: To Be Published
Title: Novel crystal structure of DHNA-CoA Thioesterase from Staphylococcus aureus
Authors: Murad, A.M. / Perbandt, M. / Lindner, J. / Schubert, R. / Mundogo, C. / Brognaro, H. / Falke, S. / Wrenger, C. / Betzel, C.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 21, 2018ID: 5LQL
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2May 8, 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

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybenzoyl-CoA thioesterase
B: 4-hydroxybenzoyl-CoA thioesterase
C: 4-hydroxybenzoyl-CoA thioesterase
D: 4-hydroxybenzoyl-CoA thioesterase


Theoretical massNumber of molelcules
Total (without water)72,7234
Polymers72,7234
Non-polymers00
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration, light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-40 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.607, 90.783, 75.378
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase family active site protein


Mass: 18180.717 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: AB520_06685, ERS072840_02738 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A166E508
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.37 Å3/Da / Density % sol: 48 % / Description: Rectangle shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES-Na pH 7.0, 1.0 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→75.33 Å / Num. obs: 164237 / % possible obs: 97.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.04 Å2 / Net I/σ(I): 19.9
Reflection shellResolution: 1.3→1.33 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→75.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.797 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19767 8701 5 %RANDOM
Rwork0.17818 ---
obs0.17917 164237 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.19 Å2
2---0.17 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.3→75.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 0 314 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.025303
X-RAY DIFFRACTIONr_bond_other_d0.0020.024916
X-RAY DIFFRACTIONr_angle_refined_deg2.6771.9527173
X-RAY DIFFRACTIONr_angle_other_deg1.192311436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52124.206252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93515985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7571525
X-RAY DIFFRACTIONr_chiral_restr0.1790.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025825
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021132
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_it2.0722.0382501
X-RAY DIFFRACTIONr_mcbond_other2.0572.0372500
X-RAY DIFFRACTIONr_mcangle_it2.8293.0553140
X-RAY DIFFRACTIONr_mcangle_other2.8283.0563141
X-RAY DIFFRACTIONr_scbond_it4.1052.482802
X-RAY DIFFRACTIONr_scbond_other4.1062.4812803
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.893.5324031
X-RAY DIFFRACTIONr_long_range_B_refined6.59424.0185918
X-RAY DIFFRACTIONr_long_range_B_other6.58823.9885910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 609 -
Rwork0.275 11872 -
obs--95.95 %

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