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- PDB-4ybv: Crystal Structure of mutant of (Q32A) thioesterase enzyme SAV0944... -

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Basic information

Entry
Database: PDB / ID: 4ybv
TitleCrystal Structure of mutant of (Q32A) thioesterase enzyme SAV0944 from Staphylococcus aureus subsp. aureus Mu50
ComponentsUncharacterized protein
KeywordsHYDROLASE / Thioesterase / Hot dog fold / Streptococcus pneumonia / Mutant
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 / 4HBT domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.
CitationJournal: To Be Published
Title: Crystal Structure of mutant of (Q32A) hypothetical protein SAV0944 from Staphylococcus aureus subsp. aureus Mu50
Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)55,1204
Polymers55,1204
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-28 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.640, 90.850, 65.150
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly confirmed by gel filtration

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Components

#1: Protein
Uncharacterized protein


Mass: 13779.903 Da / Num. of mol.: 4 / Mutation: Q32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV0944 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99VD7, UniProt: A0A0H3JUJ1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.4 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG4000, 100mM sodium citrate pH6.5, and 12%2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→29.75 Å / Num. obs: 34190 / % possible obs: 98.6 % / Redundancy: 7.4 % / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.3 % / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M20

4m20


Resolution: 2→29.747 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1701 4.98 %
Rwork0.191 --
obs0.1932 34165 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 0 223 3899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143747
X-RAY DIFFRACTIONf_angle_d1.4965071
X-RAY DIFFRACTIONf_dihedral_angle_d14.2551363
X-RAY DIFFRACTIONf_chiral_restr0.072609
X-RAY DIFFRACTIONf_plane_restr0.008638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05880.34221150.24652695X-RAY DIFFRACTION98
2.0588-2.12530.28991490.23462699X-RAY DIFFRACTION98
2.1253-2.20120.3091370.22672673X-RAY DIFFRACTION98
2.2012-2.28930.29521250.21792686X-RAY DIFFRACTION98
2.2893-2.39350.30071280.22592706X-RAY DIFFRACTION98
2.3935-2.51960.27521470.2242703X-RAY DIFFRACTION98
2.5196-2.67740.30731560.23162680X-RAY DIFFRACTION99
2.6774-2.88390.27541610.22432691X-RAY DIFFRACTION99
2.8839-3.17380.2551440.21652737X-RAY DIFFRACTION99
3.1738-3.63240.2261470.17882715X-RAY DIFFRACTION99
3.6324-4.57380.15721420.14642722X-RAY DIFFRACTION99
4.5738-29.75010.18511500.1542757X-RAY DIFFRACTION98

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