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- PDB-5lk6: Crystal structure of a lipase carboxylesterase from Sulfolobus is... -

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Basic information

Entry
Database: PDB / ID: 5lk6
TitleCrystal structure of a lipase carboxylesterase from Sulfolobus islandicus
ComponentsAlpha/beta hydrolase fold-3 domain protein
KeywordsHYDROLASE / Esterase / lipase / Sulfolobus / thermostable
Function / homology
Function and homology information


Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha/beta hydrolase fold-3 domain protein
Similarity search - Component
Biological speciesSulfolobus islandicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchwarz-Linnet, T. / Teilum, K. / Olsen, J.G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
The Danish Council for Independent Research11-106683 Denmark
CitationJournal: To Be Published
Title: EstA from Sufolobus islandicus is stabilized by mono-methylation of lysine residues
Authors: Schwarz-Linnet, T. / Stiefler-Jensen, D. / de Lichetenberg, C. / Olsen, J.G. / Nguyen, T.T.T.N. / Rand, K.D. / Teilum, K.
History
DepositionJul 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold-3 domain protein
B: Alpha/beta hydrolase fold-3 domain protein
C: Alpha/beta hydrolase fold-3 domain protein
D: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,93012
Polymers138,1624
Non-polymers7698
Water7,891438
1
A: Alpha/beta hydrolase fold-3 domain protein
B: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4656
Polymers69,0812
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-38 kcal/mol
Surface area22340 Å2
MethodPISA
2
C: Alpha/beta hydrolase fold-3 domain protein
D: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4656
Polymers69,0812
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-40 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.410, 166.410, 185.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-610-

HOH

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Components

#1: Protein
Alpha/beta hydrolase fold-3 domain protein


Mass: 34540.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Hyperthermophil acidophil archea
Source: (gene. exp.) Sulfolobus islandicus (strain REY15A) (archaea)
Strain: REY15A / Cell: Prokaryot / Cell line: E233S / Gene: SiRe_0290 / Plasmid: pSeSD
Details (production host): D-Arabinose inducible promoter, shuttle vector
Cell (production host): Prokaryot / Cell line (production host): E233S / Production host: Sulfolobus islandicus REY15A (archaea) / Strain (production host): SiRe_0290 / Variant (production host): REY15A / References: UniProt: F0NDQ1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.66 Å3/Da / Density % sol: 73.34 % / Description: Larger than 0.2 mm
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Hampton Reaserch Crystal Screen 2 (HR2-112) Condition #23. 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane. Reservoir volume 600 uL. 2 uL of EstA 10 mg/mL in 50 mM ...Details: Hampton Reaserch Crystal Screen 2 (HR2-112) Condition #23. 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane. Reservoir volume 600 uL. 2 uL of EstA 10 mg/mL in 50 mM Tris pH 8, mixed with 2 uL of reservoir volume for hanging drop at room temperature.
PH range: 6.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2012
Details: First mirror: Water-cooled vertically collimating cylindrical mirror (R = 7300 m). Second mirror: Toroid mirror for horizontal and vertical focusing (R = 3300 m, R = 27 mm).
RadiationMonochromator: Water-cooled double-crystal monochromator, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.42 Å / Num. obs: 79041 / % possible obs: 93.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 10.62 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSSeptember 26, 2012data reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AIK

3aik


Resolution: 2.6→29.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.985 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 3952 5 %RANDOM
Rwork0.15705 ---
obs0.15892 75089 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.085 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9368 0 40 438 9846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199624
X-RAY DIFFRACTIONr_bond_other_d0.0020.029216
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.97213072
X-RAY DIFFRACTIONr_angle_other_deg1.113321164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97951204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97723.585424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.402151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.651564
X-RAY DIFFRACTIONr_chiral_restr0.1130.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110868
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2342.5884828
X-RAY DIFFRACTIONr_mcbond_other2.2352.5874827
X-RAY DIFFRACTIONr_mcangle_it3.4223.8756028
X-RAY DIFFRACTIONr_mcangle_other3.4223.8766029
X-RAY DIFFRACTIONr_scbond_it3.5182.9594796
X-RAY DIFFRACTIONr_scbond_other3.4822.9474762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4424.2526996
X-RAY DIFFRACTIONr_long_range_B_refined7.08430.5310806
X-RAY DIFFRACTIONr_long_range_B_other7.00830.45110763
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 284 -
Rwork0.22 5403 -
obs--98.2 %

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