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- PDB-4wy8: Structural analysis of two fungal esterases from Rhizomucor miehe... -

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Basic information

Entry
Database: PDB / ID: 4wy8
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
Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / 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 CAU432 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 16, 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 1.3Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)146,6324
Polymers146,6324
Non-polymers00
Water9,530529
1
A: esterase
B: esterase


Theoretical massNumber of molelcules
Total (without water)73,3162
Polymers73,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-6 kcal/mol
Surface area25730 Å2
MethodPISA
2
C: esterase
D: esterase


Theoretical massNumber of molelcules
Total (without water)73,3162
Polymers73,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-6 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.125, 49.675, 183.214
Angle α, β, γ (deg.)90.00, 111.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
esterase /


Mass: 36657.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei CAU432 (fungus) / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3KKZ9*PLUS, carboxylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20% (w/v) PEG4000; 10% (v/v) 2-propanol; 100mM HEPES buffer (pH7.5)

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→46.65 Å / Num. obs: 55910 / % possible obs: 94.49 % / Redundancy: 3.7 % / Net I/σ(I): 15.08

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJI

1jji


Resolution: 2.27→46.645 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.26 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2359 2792 4.99 %
Rwork0.1884 --
obs0.1908 55905 94.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→46.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10198 0 0 529 10727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910409
X-RAY DIFFRACTIONf_angle_d1.21214180
X-RAY DIFFRACTIONf_dihedral_angle_d12.9513817
X-RAY DIFFRACTIONf_chiral_restr0.0491648
X-RAY DIFFRACTIONf_plane_restr0.0071808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30910.28411110.21241837X-RAY DIFFRACTION68
2.3091-2.35110.26761060.19822134X-RAY DIFFRACTION76
2.3511-2.39640.28281110.20542316X-RAY DIFFRACTION84
2.3964-2.44530.26381350.2082458X-RAY DIFFRACTION89
2.4453-2.49840.26711430.20862652X-RAY DIFFRACTION94
2.4984-2.55650.26711420.20812705X-RAY DIFFRACTION98
2.5565-2.62050.28991320.21322851X-RAY DIFFRACTION100
2.6205-2.69130.24581430.2062741X-RAY DIFFRACTION100
2.6913-2.77050.2751370.21822821X-RAY DIFFRACTION100
2.7705-2.85990.24391390.20362803X-RAY DIFFRACTION100
2.8599-2.96210.30541500.20292799X-RAY DIFFRACTION100
2.9621-3.08070.25661600.19882778X-RAY DIFFRACTION100
3.0807-3.22090.20811330.19652812X-RAY DIFFRACTION100
3.2209-3.39060.22221510.18612773X-RAY DIFFRACTION99
3.3906-3.6030.2641680.18532790X-RAY DIFFRACTION99
3.603-3.88110.23331460.17822760X-RAY DIFFRACTION98
3.8811-4.27140.20691420.16652763X-RAY DIFFRACTION97
4.2714-4.88890.2171560.15832744X-RAY DIFFRACTION96
4.8889-6.15720.19191480.18252791X-RAY DIFFRACTION97
6.1572-46.65440.17261390.17292785X-RAY DIFFRACTION94

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