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- PDB-4wy5: Structural analysis of two fungal esterases from Rhizomucor miehe... -

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Basic information

Entry
Database: PDB / ID: 4wy5
TitleStructural analysis of two fungal esterases from Rhizomucor miehei explaining their substrate specificity
ComponentsEsterase
KeywordsHYDROLASE / Rhizomucor miehei / Esterase / Substrate specificity
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / carboxylesterase
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
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsQin, Z. / Yang, S. / Duan, X. / Yan, Q. / Jiang, Z.
CitationJournal: J.Lipid Res. / Year: 2015
Title: Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei
Authors: Yang, S. / Qin, Z. / Duan, X. / Yan, Q. / Jiang, Z.
History
DepositionNov 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4965
Polymers72,2082
Non-polymers2883
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-35 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.691, 64.528, 64.792
Angle α, β, γ (deg.)106.81, 116.37, 103.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Esterase /


Mass: 36104.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / Plasmid: PET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5J5W4, carboxylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.74 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% (w/v)PEG3350; 0.2M (NH4)2SO4; 0.1M MES buffer pH6.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.43→31.8 Å / Num. obs: 26738 / % possible obs: 94.01 % / Redundancy: 2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.92

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data scaling
AUTOMARphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→31.8 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.56 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2256 1992 7.45 %
Rwork0.1775 --
obs0.1811 26738 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 15 269 5143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014981
X-RAY DIFFRACTIONf_angle_d1.2426803
X-RAY DIFFRACTIONf_dihedral_angle_d13.8161781
X-RAY DIFFRACTIONf_chiral_restr0.05806
X-RAY DIFFRACTIONf_plane_restr0.007872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4113-2.47160.32161220.25131511X-RAY DIFFRACTION82
2.4716-2.53840.31551400.21311718X-RAY DIFFRACTION97
2.5384-2.6130.29431400.2091769X-RAY DIFFRACTION98
2.613-2.69730.27021470.19791843X-RAY DIFFRACTION98
2.6973-2.79370.25231430.20041760X-RAY DIFFRACTION98
2.7937-2.90550.2881420.19691759X-RAY DIFFRACTION98
2.9055-3.03760.24891430.20491791X-RAY DIFFRACTION98
3.0376-3.19760.22441510.19871799X-RAY DIFFRACTION99
3.1976-3.39780.25321430.19041812X-RAY DIFFRACTION99
3.3978-3.65970.21031460.181745X-RAY DIFFRACTION99
3.6597-4.02740.20571470.15021840X-RAY DIFFRACTION99
4.0274-4.60870.18961410.1431793X-RAY DIFFRACTION99
4.6087-5.80070.19351430.15571800X-RAY DIFFRACTION99
5.8007-31.8550.18791440.17051806X-RAY DIFFRACTION99

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