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- PDB-4g4j: Crystal structure of glucuronoyl esterase S213A mutant from Sporo... -

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Basic information

Entry
Database: PDB / ID: 4g4j
TitleCrystal structure of glucuronoyl esterase S213A mutant from Sporotrichum thermophile in complex with methyl 4-O-methyl-beta-D-glucopyranuronate determined at 2.35 A resolution
Components4-O-methyl-glucuronoyl methylesterase
KeywordsHYDROLASE / Alpha/Beta Hydrolase / 3-layer alpha/beta/alpha sandwich / Rossmann Fold / Carbohydrate Binding / 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
Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
methyl 4-O-methyl-beta-D-glucopyranuronate / 4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCharavgi, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)47,69424
Polymers46,0461
Non-polymers1,64823
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.096, 69.766, 103.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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: Sugar ChemComp-MCU / methyl 4-O-methyl-beta-D-glucopyranuronate / methyl (2S,3S,4R,5R,6R)-3-methoxy-4,5,6-tris(oxidanyl)oxane-2-carboxylate


Type: D-saccharide, beta linking / Mass: 222.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O7
IdentifierTypeProgram
b-D-GlcpA4OMe6OMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.6 %
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: OTHER / Wavelength: 1.5419 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 16, 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: 2.35→13.48 Å / Num. all: 15099 / Num. obs: 15099 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.7
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2119 / % possible all: 90.4

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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: 4G4I

4g4i


Resolution: 2.35→13.44 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.845 / SU B: 8.156 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.549 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24471 760 5 %RANDOM
Rwork0.18572 ---
all0.18883 14330 --
obs0.18883 14330 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.261 Å
Refinement stepCycle: LAST / Resolution: 2.35→13.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 107 212 3055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022889
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9553893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7224.628121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86315410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5991514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212196
LS refinement shellResolution: 2.35→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 48 -
Rwork0.23 902 -
obs--89.2 %

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