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- PDB-5byu: Crystal structure of unnamed thioesterase Ipg2867 from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5byu
TitleCrystal structure of unnamed thioesterase Ipg2867 from Legionella pneumophila
ComponentsThioesterase
KeywordsHYDROLASE / Thioesterase / hotdog fold / 4HBT
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
: / Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Thioesterase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSwarbrick, C.M.D. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal structure of unnamed thioesterase Ipg2867 from Legionella pneumophila
Authors: Swarbrick, C.M.D. / Forwood, J.K.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 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_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioesterase
B: Thioesterase
C: Thioesterase
D: Thioesterase
E: Thioesterase
F: Thioesterase
G: Thioesterase
H: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,53812
Polymers121,4688
Non-polymers3,0704
Water3,207178
1
A: Thioesterase
B: Thioesterase
C: Thioesterase
D: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2696
Polymers60,7344
Non-polymers1,5352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-27 kcal/mol
Surface area21260 Å2
MethodPISA
2
E: Thioesterase
F: Thioesterase
G: Thioesterase
H: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2696
Polymers60,7344
Non-polymers1,5352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-28 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.140, 99.630, 112.142
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thioesterase


Mass: 15183.446 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2867 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 pLysS / References: UniProt: Q5ZRL4
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 40 mM citric acid, 30 mM bis-tris propane, 14% PEG 3350 and 10% glycerol

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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: Mar 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 40946 / % possible obs: 96.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.5 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2034: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QY3

3qy3


Resolution: 2.4→34.998 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 2144 5.24 %Random
Rwork0.229 ---
obs0.2314 40927 96.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→34.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7871 0 192 178 8241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118260
X-RAY DIFFRACTIONf_angle_d1.1911256
X-RAY DIFFRACTIONf_dihedral_angle_d15.6983022
X-RAY DIFFRACTIONf_chiral_restr0.0621265
X-RAY DIFFRACTIONf_plane_restr0.0061387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4008-2.45660.28361230.31222581X-RAY DIFFRACTION90
2.4566-2.51810.32151430.3012511X-RAY DIFFRACTION92
2.5181-2.58610.2921340.28442607X-RAY DIFFRACTION91
2.5861-2.66210.25451260.292570X-RAY DIFFRACTION93
2.6621-2.7480.29311170.27982583X-RAY DIFFRACTION92
2.748-2.84620.29691490.28032596X-RAY DIFFRACTION92
2.8462-2.960.30251380.27452551X-RAY DIFFRACTION92
2.96-3.09460.30351490.26392589X-RAY DIFFRACTION91
3.0946-3.25760.24441380.24822586X-RAY DIFFRACTION92
3.2576-3.46140.2431460.23222553X-RAY DIFFRACTION92
3.4614-3.72820.25151510.21022600X-RAY DIFFRACTION92
3.7282-4.10250.241450.19862604X-RAY DIFFRACTION92
4.1025-4.69420.17471290.16392581X-RAY DIFFRACTION92
4.6942-5.90670.22841320.18612634X-RAY DIFFRACTION93
5.9067-29.90110.21831550.21222648X-RAY DIFFRACTION91

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