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- PDB-3e1e: Crystal structure of a Thioesterase family protein from Silicibac... -

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Basic information

Entry
Database: PDB / ID: 3e1e
TitleCrystal structure of a Thioesterase family protein from Silicibacter pomeroyi. NorthEast Structural Genomics target SiR180A
ComponentsThioesterase family protein
KeywordsHYDROLASE / Thioesterase family protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


acyl-CoA hydrolase / acyl-CoA hydrolase activity
Similarity search - Function
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
Medium/long-chain acyl-CoA thioesterase YigI
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a Thioesterase family protein from Silicibacter pomeroyi. NorthEast Structural Genomics target SiR180A
Authors: Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioesterase family protein
B: Thioesterase family protein
C: Thioesterase family protein
D: Thioesterase family protein
E: Thioesterase family protein
F: Thioesterase family protein
G: Thioesterase family protein
H: Thioesterase family protein


Theoretical massNumber of molelcules
Total (without water)122,8058
Polymers122,8058
Non-polymers00
Water7,314406
1
A: Thioesterase family protein
B: Thioesterase family protein
F: Thioesterase family protein
H: Thioesterase family protein


Theoretical massNumber of molelcules
Total (without water)61,4024
Polymers61,4024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-47 kcal/mol
Surface area22440 Å2
MethodPISA
2
C: Thioesterase family protein
D: Thioesterase family protein
E: Thioesterase family protein
G: Thioesterase family protein


Theoretical massNumber of molelcules
Total (without water)61,4024
Polymers61,4024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-47 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.105, 107.315, 112.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thioesterase family protein


Mass: 15350.599 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO3603 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LMG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100 mM MgCl2, 100 mM Tris PH9, 22% PEG100, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 128018 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.082 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 12 / Num. unique all: 13964 / Rsym value: 0.297 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→48.39 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 93999.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 11792 9.9 %RANDOM
Rwork0.223 ---
obs0.223 119711 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6151 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---2.94 Å20 Å2
3---4.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 0 406 8932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 2075 9.6 %
Rwork0.218 19476 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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