[English] 日本語
Yorodumi
- PDB-7toh: Crystal structure of carbohydrate esterase PbeAcXE, in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7toh
TitleCrystal structure of carbohydrate esterase PbeAcXE, in complex with MeGlcpA-Xylp
ComponentsSGNH hydrolase
KeywordsHYDROLASE / carbohydrate esterase / CE / Acetyl xylan esterases / xylan esterase / AcXE
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds
Similarity search - Function
: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesProlixibacter bellariivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Jurak, E. / Master, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2022
Title: Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans.
Authors: Penttinen, L. / Kouhi, V. / Faure, R. / Skarina, T. / Stogios, P. / Master, E. / Jurak, E.
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: SGNH hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0702
Polymers42,7301
Non-polymers3401
Water12,520695
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.610, 42.810, 76.700
Angle α, β, γ (deg.)90.000, 108.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein SGNH hydrolase


Mass: 42729.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prolixibacter bellariivorans (bacteria)
Gene: PbJCM13498_02590 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A5M4AV20
#2: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 340.281 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 mM acetylated xylooligosaccharides, 0.1 M Tris pH 6.5 and 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.26→28.53 Å / Num. obs: 93487 / % possible obs: 97.4 % / Redundancy: 11.8 % / Biso Wilson estimate: 16.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Net I/σ(I): 13.6
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6513 / CC1/2: 0.557 / Rpim(I) all: 0.583 / % possible all: 92.4

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
HKL-3000phasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.26→28.53 Å / SU ML: 0.1258 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.1006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.169 4703 5.03 %RANDOM
Rwork0.1346 88753 --
obs0.1363 93456 97.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 1.26→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 23 695 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01243061
X-RAY DIFFRACTIONf_angle_d1.37324162
X-RAY DIFFRACTIONf_chiral_restr0.112469
X-RAY DIFFRACTIONf_plane_restr0.0124538
X-RAY DIFFRACTIONf_dihedral_angle_d13.01761147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.270.28371380.25982727X-RAY DIFFRACTION92.09
1.27-1.290.2731380.25092821X-RAY DIFFRACTION92.27
1.29-1.310.25661640.2442846X-RAY DIFFRACTION94.62
1.31-1.320.29121590.22382863X-RAY DIFFRACTION95.48
1.32-1.340.23861540.21532903X-RAY DIFFRACTION95.17
1.34-1.360.20191440.1992877X-RAY DIFFRACTION96.15
1.36-1.380.23451430.18832922X-RAY DIFFRACTION95.51
1.38-1.40.22041660.17522892X-RAY DIFFRACTION96.86
1.4-1.420.21621590.16792933X-RAY DIFFRACTION96.32
1.42-1.440.19231550.15822931X-RAY DIFFRACTION97.29
1.44-1.470.18641360.14982932X-RAY DIFFRACTION96.39
1.47-1.490.17991530.13832950X-RAY DIFFRACTION97.7
1.49-1.520.16871490.12922921X-RAY DIFFRACTION96.6
1.52-1.550.1741550.12232968X-RAY DIFFRACTION98.11
1.55-1.590.17131590.11682951X-RAY DIFFRACTION96.7
1.59-1.620.15161600.11452959X-RAY DIFFRACTION98.48
1.62-1.670.16121330.12482985X-RAY DIFFRACTION97.77
1.67-1.710.15341580.11632986X-RAY DIFFRACTION97.46
1.71-1.760.14951950.12032943X-RAY DIFFRACTION99.18
1.76-1.820.16991530.11572991X-RAY DIFFRACTION98.19
1.82-1.880.15941610.11752974X-RAY DIFFRACTION98.21
1.88-1.960.15311690.11932993X-RAY DIFFRACTION98.57
1.96-2.050.15131750.1233010X-RAY DIFFRACTION98.97
2.05-2.150.15171530.1183024X-RAY DIFFRACTION99.22
2.15-2.290.15051550.11793019X-RAY DIFFRACTION99.44
2.29-2.470.16261650.1293046X-RAY DIFFRACTION99.63
2.47-2.710.17331760.13793039X-RAY DIFFRACTION99.54
2.71-3.110.16051530.14023075X-RAY DIFFRACTION99.78
3.11-3.910.14741530.12153114X-RAY DIFFRACTION99.97
3.91-28.530.18591720.14293158X-RAY DIFFRACTION99.67

+
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