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- PDB-4i82: Crystal Structure of Hypothetical Thioesterase Protein SP_1851 fr... -

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Basic information

Entry
Database: PDB / ID: 4i82
TitleCrystal Structure of Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / PaaI/YdiI-like / Hot Dog Fold / thioesterase
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
Thioesterase domain-containing protein / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKhandokar, Y.B. / Forwood, J.K.
CitationJournal: To be published
Title: Crystal Structure of Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
Authors: Khandokar, Y.B. / Forwood, J.K.
History
DepositionDec 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)30,4712
Polymers30,4712
Non-polymers00
Water00
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein

A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)60,9414
Polymers60,9414
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8010 Å2
ΔGint-26 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.260, 118.470, 87.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative uncharacterized protein / Hypothetical Thioesterase Protein SP1851


Mass: 15235.274 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1851 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3pLyse / References: UniProt: Q97NZ8, UniProt: A0A0H2URF0*PLUS

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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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200mM Ammonium Tartrate dibasic, 20% PEG 3350, 100mM Tris pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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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: Oct 9, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→35.22 Å / Num. all: 8714 / Num. obs: 8159 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.49→2.62 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LBB

3lbb


Resolution: 2.5→24.77 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.567 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 1.174 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28603 374 4.6 %RANDOM
Rwork0.23846 ---
obs0.24074 7735 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 0 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191832
X-RAY DIFFRACTIONr_bond_other_d0.0060.021725
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9362479
X-RAY DIFFRACTIONr_angle_other_deg0.9133944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6195240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54625.65876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.11615300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.342153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 17 -
Rwork0.265 514 -
obs--84.15 %

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