[English] 日本語
Yorodumi
- PDB-9fkj: The structure of glycosynthase IXT6 (E241G mutant), the intracell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fkj
TitleThe structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6 in complex with two xylobiose-F molecules
ComponentsBeta-xylanase
KeywordsHYDROLASE / IXT6 / glycosynthase / Geobacillus proteiniphilus T-6 / Geobacillus stearothermophilus
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesGeobacillus proteiniphilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHadad, N. / Chmelnik, O. / Dessau, M. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6 in complex with two xylobiose-F molecules
Authors: Hadad, N. / Chmelnik, O. / Dessau, M. / Shoham, Y. / Shoham, G.
History
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3758
Polymers77,2462
Non-polymers1,1296
Water13,565753
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4686
Polymers38,6231
Non-polymers8455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9072
Polymers38,6231
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.165, 80.602, 79.307
Angle α, β, γ (deg.)90.000, 92.218, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Beta-xylanase


Mass: 38622.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus proteiniphilus (bacteria) / Gene: xynA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09LY9, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-1-fluoro-D-xylopyranose


Type: oligosaccharide / Mass: 284.236 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
[][<C5O3F1>]{[(1+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#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.: 753 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Sodium acetate and 0.1M Sodium cacodylate buffer at pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→79.25 Å / Num. obs: 71422 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.81 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Rrim(I) all: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4614 / CC1/2: 0.81 / Rpim(I) all: 0.3 / Rrim(I) all: 0.58

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→79.25 Å / SU ML: 0.2056 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.2006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 3573 5.01 %
Rwork0.1631 67802 -
obs0.1649 71375 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.86 Å2
Refinement stepCycle: LAST / Resolution: 2→79.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 75 753 6240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075671
X-RAY DIFFRACTIONf_angle_d0.88227692
X-RAY DIFFRACTIONf_chiral_restr0.0559812
X-RAY DIFFRACTIONf_plane_restr0.0055993
X-RAY DIFFRACTIONf_dihedral_angle_d7.0965779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.25771280.24352609X-RAY DIFFRACTION99.35
2.03-2.050.29371440.22662586X-RAY DIFFRACTION99.31
2.05-2.080.27651250.21882639X-RAY DIFFRACTION99
2.08-2.110.23551250.21222587X-RAY DIFFRACTION99.27
2.11-2.150.23351410.20372584X-RAY DIFFRACTION99.24
2.15-2.180.27991420.20352633X-RAY DIFFRACTION99.53
2.18-2.220.22651490.18912558X-RAY DIFFRACTION99.3
2.22-2.260.22641290.18922601X-RAY DIFFRACTION99.24
2.26-2.30.22441320.18522632X-RAY DIFFRACTION99.21
2.3-2.350.22161300.18242605X-RAY DIFFRACTION99.35
2.35-2.40.23361620.18552610X-RAY DIFFRACTION99.46
2.4-2.460.21331430.17762590X-RAY DIFFRACTION99.2
2.46-2.520.2431310.17492613X-RAY DIFFRACTION99.42
2.52-2.590.22611260.1752596X-RAY DIFFRACTION99.45
2.59-2.660.2471370.18312614X-RAY DIFFRACTION99.53
2.66-2.750.20341400.182642X-RAY DIFFRACTION99.5
2.75-2.850.24191220.18052601X-RAY DIFFRACTION99.52
2.85-2.960.23391380.18072618X-RAY DIFFRACTION99.57
2.96-3.10.20691520.17762590X-RAY DIFFRACTION99.24
3.1-3.260.23581490.16632603X-RAY DIFFRACTION98.78
3.26-3.460.20971320.1562624X-RAY DIFFRACTION98.64
3.46-3.730.1661340.13882595X-RAY DIFFRACTION98.81
3.73-4.110.13671660.12242560X-RAY DIFFRACTION97.92
4.11-4.70.14561350.1192633X-RAY DIFFRACTION98.61
4.7-5.920.15531350.14042626X-RAY DIFFRACTION98.47
5.92-79.250.16841260.15212653X-RAY DIFFRACTION96.69

+
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