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- PDB-4g4i: Crystal structure of glucuronoyl esterase S213A mutant from Sporo... -

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Basic information

Entry
Database: PDB / ID: 4g4i
TitleCrystal structure of glucuronoyl esterase S213A mutant from Sporotrichum thermophile determined at 1.9 A resolution
Components4-O-methyl-glucuronoyl methylesterase
KeywordsHYDROLASE / Alpha/Beta Hydrolase / 3-layer alpha/beta/alpha sandwich / Rossmann Fold / Glucuronoyl esterase
Function / homology
Function and homology information


(4-O-methyl)-D-glucuronate-lignin esterase / lignin catabolic process / carboxylic ester hydrolase activity / extracellular region
Similarity search - Function
: / Glucuronyl esterase, fungi / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCharvagi, M.D. / Dimarogona, M. / Topakas, E. / Christakopoulos, P. / Chrysina, E.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst.
Authors: Charavgi, M.D. / Dimarogona, M. / Topakas, E. / Christakopoulos, P. / Chrysina, E.D.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source / _diffrn_source.type
Revision 1.3Sep 13, 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,81912
Polymers46,0461
Non-polymers77311
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.010, 69.616, 103.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-928-

HOH

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Components

#1: Protein 4-O-methyl-glucuronoyl methylesterase


Mass: 46046.168 Da / Num. of mol.: 1 / Mutation: S213A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (fungus) / Strain: ATCC 42464 / Gene: MYCTH_55568 / Plasmid: pPICZalphaC / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: G2QJR6, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEGMENT CORRESPONDS TO A C-MYC EPITOPE

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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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% PEG 550 MME, 0.1M sodium acetate , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.5419 Å
DetectorType: Atlas 135mm CCD detector / Detector: CCD / Date: Nov 11, 2011 / Details: Mutlti-layer Xray optic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→13.97 Å / Num. all: 30113 / Num. obs: 30113 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / Num. unique all: 4161 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.6.0117refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G4G

4g4g


Resolution: 1.9→13.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.827 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20758 1524 5.1 %RANDOM
Rwork0.16894 ---
all0.17088 28557 --
obs0.17088 28557 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.199 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 1.9→13.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 50 437 3223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192874
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9453906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64624.628121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212219
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 90 -
Rwork0.212 1811 -
obs--92.82 %

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