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

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Basic information

Entry
Database: PDB / ID: 4zrf
TitleCrystal Structure of Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
ComponentsHypothetical Thioesterase Protein SP_1851
KeywordsHYDROLASE / PaaI thioesterase / Hotdog fold / Streptococcus pneumoniae
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
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal Structure of Hypothetical Thioesterase Protein SP_1851 from Streptococcus pneumoniae TIGR4
Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.K.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site ..._diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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: Hypothetical Thioesterase Protein SP_1851
B: Hypothetical Thioesterase Protein SP_1851


Theoretical massNumber of molelcules
Total (without water)30,4712
Polymers30,4712
Non-polymers00
Water3,441191
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)60,9414
Polymers60,9414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7830 Å2
ΔGint-29 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.180, 118.440, 86.640
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 Hypothetical Thioesterase Protein SP_1851 / Paal Thioesterase


Mass: 15235.274 Da / Num. of mol.: 2
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: A0A0M3KL39*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200mM Ammonium Tartrate dibasic, 20% PEG 3350, 100mM Tris pH7.5
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.86→59.01 Å / Num. obs: 20211 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.7
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LBB

3lbb


Resolution: 1.86→24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25391 1019 5 %RANDOM
Rwork0.21638 ---
obs0.21825 19187 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.072 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.86→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 0 191 2030
LS refinement shellResolution: 1.859→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 70 -
Rwork0.278 1391 -
obs--99.32 %

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