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- PDB-3aik: Crystal structure of a HSL-like carboxylesterase from Sulfolobus ... -

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Basic information

Entry
Database: PDB / ID: 3aik
TitleCrystal structure of a HSL-like carboxylesterase from Sulfolobus tokodaii
Components303aa long hypothetical esterase
KeywordsHYDROLASE / Carboxylesterase / thermophilic / dimer / archaea
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: 1.95 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)145,70819
Polymers144,0524
Non-polymers1,65715
Water11,367631
1
A: 303aa long hypothetical esterase
D: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7849
Polymers72,0262
Non-polymers7587
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)72,92510
Polymers72,0262
Non-polymers8998
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)72,90210
Polymers72,0262
Non-polymers8768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-16 kcal/mol
Surface area21600 Å2
MethodPISA
4
C: 303aa long hypothetical esterase
D: 303aa long hypothetical esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8079
Polymers72,0262
Non-polymers7817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.327, 114.752, 102.206
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
303aa long hypothetical esterase / Carboxylesterase


Mass: 36012.949 Da / Num. of mol.: 4
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


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
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: BL44B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2009
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 120550 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.085 / Rsym value: 0.064 / Net I/σ(I): 22.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.1 / Num. unique all: 11631 / Rsym value: 0.421 / % possible all: 97.7

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Processing

Software
NameVersionClassification
BL44XUBSSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJI

1jji


Resolution: 1.95→44.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.565 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.19361 6045 5 %RANDOM
Rwork0.15903 ---
obs0.16077 113863 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.985 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.19 Å2
2---0.12 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8948 0 105 631 9684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229261
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.97112576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47851128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98123.981432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.574151480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0051548
X-RAY DIFFRACTIONr_chiral_restr0.1010.21366
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0217076
X-RAY DIFFRACTIONr_mcbond_it1.6961.55616
X-RAY DIFFRACTIONr_mcangle_it2.63929056
X-RAY DIFFRACTIONr_scbond_it4.39833645
X-RAY DIFFRACTIONr_scangle_it6.6714.53520
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 433 -
Rwork0.221 8342 -
obs--97.75 %

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