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- PDB-4xy5: Crystal Structure of mutant (Asp52Ala) Hypothetical Thioesterase ... -

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Basic information

Entry
Database: PDB / ID: 4xy5
TitleCrystal Structure of mutant (Asp52Ala) Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
ComponentsHypothetical Thioesterase Protein SP_1851
KeywordsHYDROLASE / Thioesterase / Streptococcus pneumoniae / PaaI
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
Acyl-coenzyme A thioesterase 13 / 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
Hypothetical Thioesterase Protein SP_1851 / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal Structure of mutant (Asp52Ala) Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.K.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / 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 / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical Thioesterase Protein SP_1851
B: Hypothetical Thioesterase Protein SP_1851


Theoretical massNumber of molelcules
Total (without water)30,3832
Polymers30,3832
Non-polymers00
Water3,009167
1
A: Hypothetical Thioesterase Protein SP_1851
B: Hypothetical Thioesterase Protein SP_1851

A: Hypothetical Thioesterase Protein SP_1851
B: Hypothetical Thioesterase Protein SP_1851


Theoretical massNumber of molelcules
Total (without water)60,7654
Polymers60,7654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area7940 Å2
ΔGint-35 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.006, 45.594, 112.368
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

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Components

#1: Protein Hypothetical Thioesterase Protein SP_1851


Mass: 15191.265 Da / Num. of mol.: 2 / Mutation: D52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1851 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97NZ8, UniProt: A0A0M3KL07*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.93 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, 100mM HEPES pH7.5, 200mM Magnesium Chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9196 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.8→31.98 Å / Num. obs: 20838 / % possible obs: 97.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 11.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I82

4i82


Resolution: 1.8→28.884 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 1037 4.98 %
Rwork0.1816 --
obs0.184 20832 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 167 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071872
X-RAY DIFFRACTIONf_angle_d0.9972532
X-RAY DIFFRACTIONf_dihedral_angle_d12.411658
X-RAY DIFFRACTIONf_chiral_restr0.043302
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.89490.27741590.19642779X-RAY DIFFRACTION98
1.8949-2.01360.24861260.1812825X-RAY DIFFRACTION98
2.0136-2.16910.24281480.182829X-RAY DIFFRACTION98
2.1691-2.38730.21031570.17512818X-RAY DIFFRACTION99
2.3873-2.73250.23181500.18682849X-RAY DIFFRACTION99
2.7325-3.44170.24041630.17882842X-RAY DIFFRACTION99
3.4417-28.88790.21271340.18152853X-RAY DIFFRACTION96

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