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- PDB-3aim: R267E mutant of a HSL-like carboxylesterase from Sulfolobus tokodaii -

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Basic information

Entry
Database: PDB / ID: 3aim
TitleR267E mutant of a HSL-like carboxylesterase from Sulfolobus tokodaii
Components303aa long hypothetical esterase
KeywordsHYDROLASE / Carboxylesterase / thermophilic / dimer / archaea / R267E
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / identical protein binding
Similarity search - Function
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
PHOSPHATE ION / Carboxylesterase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAngkawidjaja, C. / Kanaya, S.
CitationJournal: Febs J. / Year: 2012
Title: Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobustokodaii
Authors: Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionMay 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Nov 1, 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 303aa long hypothetical esterase
B: 303aa long hypothetical esterase
C: 303aa long hypothetical esterase
D: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,59619
Polymers143,9394
Non-polymers1,65715
Water2,846158
1
A: 303aa long hypothetical esterase
D: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6098
Polymers71,9702
Non-polymers6396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 303aa long hypothetical esterase
C: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98711
Polymers71,9702
Non-polymers1,0179
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 303aa long hypothetical esterase
B: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84610
Polymers71,9702
Non-polymers8768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-17 kcal/mol
Surface area22120 Å2
MethodPISA
4
C: 303aa long hypothetical esterase
D: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7519
Polymers71,9702
Non-polymers7817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-16 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.213, 114.835, 102.219
Angle α, β, γ (deg.)90.00, 109.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
303aa long hypothetical esterase / Carboxylesterase


Mass: 35984.867 Da / Num. of mol.: 4 / Mutation: R267E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST0071 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q976W8, carboxylesterase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 0.2M Ammonium phosphate monobasic, 50% MPD , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 71172 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BL38B1BSSdata collection
MOLREPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AIK

3aik


Resolution: 2.3→32.46 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.502 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.217
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24871 3588 5 %RANDOM
Rwork0.20963 ---
obs0.21155 67472 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å21.68 Å2
2---0.93 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8940 0 105 158 9203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.97112568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3751128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18224.167432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.024151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1671544
X-RAY DIFFRACTIONr_chiral_restr0.0790.21366
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0217072
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.7011.55616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.77129056
X-RAY DIFFRACTIONr_scbond_it4.68233637
X-RAY DIFFRACTIONr_scangle_it6.84.53512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 198 -
Rwork0.303 3500 -
obs--68.7 %

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