[English] 日本語
Yorodumi
- PDB-4g4j: Crystal structure of glucuronoyl esterase S213A mutant from Sporo... -

+
Open data


ID or keywords:

Loading...

-
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
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
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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY
Sequence detailsTHIS SEGMENT CORRESPONDS TO A C-MYC EPITOPE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more