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- PDB-5mif: Crystal structure of carboxyl esterase 2 (TmelEST2) from mycorrhi... -

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Basic information

Entry
Database: PDB / ID: 5mif
TitleCrystal structure of carboxyl esterase 2 (TmelEST2) from mycorrhizal fungus Tuber melanosporum
Components'Carboxyl esterase 2
KeywordsHYDROLASE / lipase alpha/beta hydrolase fold archaebacterial-like enzymes
Function / homology
Function and homology information


: / 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
(Perigord truffle) hypothetical protein
Similarity search - Component
Biological speciesTuber melanosporum Mel28 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.141 Å
AuthorsZanotti, G. / Vallese, F. / Cavazzini, D. / Ottonello, S.
CitationJournal: Sci Rep / Year: 2017
Title: A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum.
Authors: Cavazzini, D. / Grossi, G. / Levati, E. / Vallese, F. / Montanini, B. / Bolchi, A. / Zanotti, G. / Ottonello, S.
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Structure summary / Category: audit_author / citation / Item: _audit_author.name / _citation.title
Revision 1.2May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 'Carboxyl esterase 2
B: 'Carboxyl esterase 2
C: 'Carboxyl esterase 2
D: 'Carboxyl esterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,4806
Polymers149,7754
Non-polymers7052
Water12,466692
1
A: 'Carboxyl esterase 2
C: 'Carboxyl esterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2403
Polymers74,8872
Non-polymers3531
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 'Carboxyl esterase 2
D: 'Carboxyl esterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2403
Polymers74,8872
Non-polymers3531
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.898, 158.898, 226.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-504-

HOH

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Components

#1: Protein
'Carboxyl esterase 2


Mass: 37443.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tuber melanosporum Mel28 (fungus) / Gene: GSTUM_00003552001 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RIL / References: UniProt: D5GA36
#2: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 18 mg/ml in 25 mM Tris-HCl pH 8.0, 0.1M NaCl, 2% v/v Triton X-100) and 20% polyethylene glycol 3350 in 0.2 M KNO3 (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→47.28 Å / Num. obs: 93001 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 71.46
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIXdev_1647refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house

Resolution: 2.141→47.276 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.95
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 8795 4.99 %Random selection
Rwork0.1805 ---
obs0.1819 176177 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.141→47.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9227 0 50 692 9969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089505
X-RAY DIFFRACTIONf_angle_d1.15912929
X-RAY DIFFRACTIONf_dihedral_angle_d13.0073497
X-RAY DIFFRACTIONf_chiral_restr0.0491454
X-RAY DIFFRACTIONf_plane_restr0.0071672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1407-2.1650.30222850.26355289X-RAY DIFFRACTION94
2.165-2.19050.27832910.25175596X-RAY DIFFRACTION100
2.1905-2.21720.2712970.24315608X-RAY DIFFRACTION100
2.2172-2.24530.28952920.2425571X-RAY DIFFRACTION100
2.2453-2.27480.28992960.23095617X-RAY DIFFRACTION100
2.2748-2.3060.25362920.22815585X-RAY DIFFRACTION100
2.306-2.33890.28092960.22055551X-RAY DIFFRACTION100
2.3389-2.37380.22822920.2175613X-RAY DIFFRACTION100
2.3738-2.41090.26413020.21725613X-RAY DIFFRACTION100
2.4109-2.45040.25392920.20385543X-RAY DIFFRACTION100
2.4504-2.49270.25582880.22175598X-RAY DIFFRACTION100
2.4927-2.5380.23452870.22055603X-RAY DIFFRACTION100
2.538-2.58680.22372960.20545583X-RAY DIFFRACTION100
2.5868-2.63960.26132920.20285625X-RAY DIFFRACTION100
2.6396-2.6970.23552960.20175580X-RAY DIFFRACTION100
2.697-2.75970.25292900.18935565X-RAY DIFFRACTION100
2.7597-2.82870.21792940.20315596X-RAY DIFFRACTION100
2.8287-2.90520.23692940.21145561X-RAY DIFFRACTION100
2.9052-2.99070.2332910.20555612X-RAY DIFFRACTION100
2.9907-3.08720.24782940.21195564X-RAY DIFFRACTION100
3.0872-3.19750.26572970.20825600X-RAY DIFFRACTION100
3.1975-3.32550.23072940.20125602X-RAY DIFFRACTION100
3.3255-3.47680.22492970.18575585X-RAY DIFFRACTION100
3.4768-3.66010.19532880.18485579X-RAY DIFFRACTION100
3.6601-3.88930.2172880.17195617X-RAY DIFFRACTION100
3.8893-4.18940.17193000.14875604X-RAY DIFFRACTION100
4.1894-4.61070.14682930.13285561X-RAY DIFFRACTION100
4.6107-5.27710.16232930.13635592X-RAY DIFFRACTION100
5.2771-6.64560.16272970.14845599X-RAY DIFFRACTION100
6.6456-47.2880.15352910.14895570X-RAY DIFFRACTION99

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