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

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Basic information

Entry
Database: PDB / ID: 5mii
TitleCrystal structure of carboxyl esterase 2 (TmelEST2) from mycorrhizal fungus Tuber melanosporum
ComponentsCarboxyl esterase 2
KeywordsHYDROLASE / lipase alpha/beta hydrolase fold archaebacterial-like enzymes PMSF
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / (Perigord truffle) hypothetical protein
Function and homology information
Biological speciesTuber melanosporum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.372 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 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxyl esterase 2
B: Carboxyl esterase 2
C: Carboxyl esterase 2
D: Carboxyl esterase 2


Theoretical massNumber of molelcules
Total (without water)150,3914
Polymers150,3914
Non-polymers00
Water8,845491
1
A: Carboxyl esterase 2
C: Carboxyl esterase 2


Theoretical massNumber of molelcules
Total (without water)75,1962
Polymers75,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-9 kcal/mol
Surface area22960 Å2
MethodPISA
2
B: Carboxyl esterase 2
D: Carboxyl esterase 2


Theoretical massNumber of molelcules
Total (without water)75,1962
Polymers75,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-8 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.931, 157.931, 231.410
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-529-

HOH

21C-535-

HOH

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Components

#1: Protein
Carboxyl esterase 2


Mass: 37597.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tuber melanosporum (strain Mel28) (fungus)
Strain: Mel28 / Gene: GSTUM_00003552001 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: D5GA36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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 of purified protein 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: ESRF / Beamline: ID29 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.37→47.2 Å / Num. obs: 68933 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 11.8
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.372→47.198 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 3484 5.06 %random selection
Rwork0.1942 ---
obs0.1967 68822 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.372→47.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 0 491 9887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089634
X-RAY DIFFRACTIONf_angle_d1.1513121
X-RAY DIFFRACTIONf_dihedral_angle_d13.7263551
X-RAY DIFFRACTIONf_chiral_restr0.0441476
X-RAY DIFFRACTIONf_plane_restr0.0071705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3724-2.40490.40281160.32212211X-RAY DIFFRACTION86
2.4049-2.43920.33441220.29112566X-RAY DIFFRACTION98
2.4392-2.47570.35551480.28032583X-RAY DIFFRACTION100
2.4757-2.51430.31751510.26212563X-RAY DIFFRACTION100
2.5143-2.55560.29721340.25572576X-RAY DIFFRACTION100
2.5556-2.59960.30851390.2462597X-RAY DIFFRACTION100
2.5996-2.64690.28871370.22782588X-RAY DIFFRACTION100
2.6469-2.69780.30251450.22182588X-RAY DIFFRACTION100
2.6978-2.75290.26671370.22712601X-RAY DIFFRACTION100
2.7529-2.81270.25591360.23052599X-RAY DIFFRACTION100
2.8127-2.87810.32231250.23322629X-RAY DIFFRACTION100
2.8781-2.95010.31551320.23722599X-RAY DIFFRACTION100
2.9501-3.02980.30381430.23692605X-RAY DIFFRACTION100
3.0298-3.1190.30021290.23332621X-RAY DIFFRACTION100
3.119-3.21960.33041490.21732619X-RAY DIFFRACTION100
3.2196-3.33470.24451230.21942621X-RAY DIFFRACTION100
3.3347-3.46810.26231570.20942618X-RAY DIFFRACTION100
3.4681-3.62590.27231390.19362616X-RAY DIFFRACTION100
3.6259-3.8170.22941390.19782636X-RAY DIFFRACTION100
3.817-4.05610.22451480.17122649X-RAY DIFFRACTION100
4.0561-4.3690.19661380.14552667X-RAY DIFFRACTION100
4.369-4.80830.17451550.13712655X-RAY DIFFRACTION100
4.8083-5.50320.18821430.14962696X-RAY DIFFRACTION100
5.5032-6.92990.20831630.16642718X-RAY DIFFRACTION100
6.9299-47.20780.18791360.16532917X-RAY DIFFRACTION99

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