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- PDB-5dio: Crystal structure of unnamed thioesterase lpg2867 from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5dio
TitleCrystal structure of unnamed thioesterase lpg2867 from Legionella pneumophila, the D21A mutant
ComponentsThioesterase
KeywordsHYDROLASE / THIOESTERASE / HOTDOG FOLD / 4HBT
Function / homologyThioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / : / Thioesterase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSwarbrick, C.M.D. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal structure of unnamed thioesterase lpg2867 from Legionella pneumophila, the D21A mutant
Authors: Swarbrick, C.M.D. / Forwood, J.K.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _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


Theoretical massNumber of molelcules
Total (without water)30,2792
Polymers30,2792
Non-polymers00
Water00
1
A: Thioesterase
B: Thioesterase

A: Thioesterase
B: Thioesterase


Theoretical massNumber of molelcules
Total (without water)60,5584
Polymers60,5584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area5740 Å2
ΔGint-22 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.880, 115.741, 58.350
Angle α, β, γ (deg.)90.00, 115.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioesterase


Mass: 15139.437 Da / Num. of mol.: 2 / Mutation: D21A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lp12_2856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UUB5, UniProt: Q5ZRL4*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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 10% 2-propanol, 19% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→57.87 Å / Num. obs: 9199 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
Blu-Icedata collection
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BYU

5byu


Resolution: 2.6→57.87 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.885 / SU B: 0.012 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28633 478 5.2 %RANDOM
Rwork0.24888 ---
obs0.25069 8720 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.476 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å2-0.13 Å2
2--1.99 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→57.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 0 1911
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 46 -
Rwork0.355 626 -
obs--98.39 %

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