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- PDB-4xy6: Crystal Structure of mutant (Thr68Ala) Hypothetical Thioesterase ... -

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Basic information

Entry
Database: PDB / ID: 4xy6
TitleCrystal Structure of mutant (Thr68Ala) Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
ComponentsHypothetical Thioesterase Protein SP_1851
KeywordsHYDROLASE / Thioesterase / Hot dog fold / Streptococcus pneumonia / Mutant
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: 2 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal Structure of mutant (Thr68Ala) Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
Authors: Khandokar, Y.B.
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


Theoretical massNumber of molelcules
Total (without water)15,2051
Polymers15,2051
Non-polymers00
Water2,432135
1
A: Hypothetical Thioesterase Protein SP_1851

A: Hypothetical Thioesterase Protein SP_1851

A: Hypothetical Thioesterase Protein SP_1851

A: Hypothetical Thioesterase Protein SP_1851


Theoretical massNumber of molelcules
Total (without water)60,8214
Polymers60,8214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_456-x-1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area8180 Å2
ΔGint-35 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.370, 119.180, 48.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-225-

HOH

31A-255-

HOH

41A-281-

HOH

51A-285-

HOH

61A-307-

HOH

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Components

#1: Protein Hypothetical Thioesterase Protein SP_1851


Mass: 15205.249 Da / Num. of mol.: 1 / Mutation: T68A
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: A0A0M3KL08*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG3350, 100mM Tris pH6.0, 200mM magnesium chloride.

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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: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→30.17 Å / Num. obs: 9368 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 8.3 / % possible all: 99.9

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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: 2→25.576 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 466 4.97 %
Rwork0.1783 --
obs0.1803 9368 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→25.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 135 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007953
X-RAY DIFFRACTIONf_angle_d0.8991290
X-RAY DIFFRACTIONf_dihedral_angle_d11.973336
X-RAY DIFFRACTIONf_chiral_restr0.035152
X-RAY DIFFRACTIONf_plane_restr0.004165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.28930.27711830.18812888X-RAY DIFFRACTION100
2.2893-2.88360.24451420.19082941X-RAY DIFFRACTION100
2.8836-25.57770.17671410.16753073X-RAY DIFFRACTION99

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