[English] 日本語
Yorodumi
- PDB-9j4j: Crystal structure of GH9l Inulin fructotransferases(IFTase)incomp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j4j
TitleCrystal structure of GH9l Inulin fructotransferases(IFTase)incomplex with nystose(F3)
ComponentsDFA-III-forming inulin fructotransferase
KeywordsCARBOHYDRATE / IFTase / catalytic pathway / HYDROLASE
Function / homology
Function and homology information


inulin fructotransferase (DFA-III-forming) / inulin fructotransferase (DFA-III-forming) activity / transferase activity
Similarity search - Function
Inulin fructotransferase, beta helix repeat / Beta helix repeat of Inulin fructotransferase / Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / Pectin lyase fold / Pectin lyase fold/virulence factor / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
nystose / beta-D-fructofuranose / DFA-III-forming inulin fructotransferase
Similarity search - Component
Biological speciesPaenarthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsChen, G. / Wang, Z.X. / Yang, Y.Q. / Li, Y.G. / Zhang, T. / Ouyang, S.Y. / Zhang, L. / Chen, Y. / Ruan, X.L. / Miao, M.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of Sciences2018YFC1602101 China
National Natural Science Foundation of China (NSFC)31972029 China
National Natural Science Foundation of China (NSFC)31770948 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Elucidation of the mechanism underlying the sequential catalysis of inulin by fructotransferase.
Authors: Chen, G. / Wang, Z.X. / Yang, Y. / Li, Y. / Zhang, T. / Ouyang, S. / Zhang, L. / Chen, Y. / Ruan, X. / Miao, M.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DFA-III-forming inulin fructotransferase
B: DFA-III-forming inulin fructotransferase
C: DFA-III-forming inulin fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,00311
Polymers129,6433
Non-polymers4,3608
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint47 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.642, 167.642, 85.297
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

-
Protein / Non-polymers , 2 types, 17 molecules ABC

#1: Protein DFA-III-forming inulin fructotransferase


Mass: 43214.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter aurescens (bacteria) / Gene: ift / Production host: Escherichia coli (E. coli)
References: UniProt: F8QV43, inulin fructotransferase (DFA-III-forming)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 4 types, 8 molecules

#2: Polysaccharide beta-D-fructofuranose-(1-1)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb1-1DFrufb2-Glycam Condensed SequenceGMML 1.0
[][b-D-Araf]{}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 666.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: nystose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-Glycam Condensed SequenceGMML 1.0
[][b-D-Fruf]{}LINUCSPDB-CARE
#5: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density meas: 53.91 Mg/m3 / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate 0.1 M Tris (pH 8.5) 25% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 33668 / % possible obs: 100 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.22
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.495 / Num. unique obs: 1682

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.803→48.441 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.101 / SU ML: 0.208 / Cross valid method: FREE R-VALUE / ESU R Free: 0.322
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2079 1701 5.059 %
Rwork0.1582 31924 -
all0.161 --
obs-33625 99.736 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.011 Å20.005 Å20 Å2
2--0.011 Å2-0 Å2
3----0.034 Å2
Refinement stepCycle: LAST / Resolution: 2.803→48.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9081 0 293 14 9388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139588
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178880
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.68213047
X-RAY DIFFRACTIONr_angle_other_deg1.21.61520451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.32551206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31522.372468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.856151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3351560
X-RAY DIFFRACTIONr_chiral_restr0.0610.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022115
X-RAY DIFFRACTIONr_nbd_refined0.1940.21648
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.28863
X-RAY DIFFRACTIONr_nbtor_refined0.1540.24443
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.212
X-RAY DIFFRACTIONr_nbd_other0.2350.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.22
X-RAY DIFFRACTIONr_mcbond_it1.8713.244833
X-RAY DIFFRACTIONr_mcbond_other1.8713.244832
X-RAY DIFFRACTIONr_mcangle_it2.8924.8596036
X-RAY DIFFRACTIONr_mcangle_other2.8924.8596037
X-RAY DIFFRACTIONr_scbond_it2.4283.5644755
X-RAY DIFFRACTIONr_scbond_other2.4283.5644755
X-RAY DIFFRACTIONr_scangle_it3.5885.2717011
X-RAY DIFFRACTIONr_scangle_other3.5885.2727012
X-RAY DIFFRACTIONr_lrange_it5.09138.8879475
X-RAY DIFFRACTIONr_lrange_other5.09138.8899476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-2.8760.2881120.1492305X-RAY DIFFRACTION97.7751
2.876-2.9550.1981330.1462295X-RAY DIFFRACTION100
2.955-3.040.236950.1532253X-RAY DIFFRACTION100
3.04-3.1340.2031210.1642146X-RAY DIFFRACTION100
3.134-3.2370.21210.1512086X-RAY DIFFRACTION100
3.237-3.350.1941150.1472034X-RAY DIFFRACTION100
3.35-3.4770.219960.1491979X-RAY DIFFRACTION100
3.477-3.6180.1941130.1461876X-RAY DIFFRACTION100
3.618-3.7790.244940.1411797X-RAY DIFFRACTION99.9472
3.779-3.9640.208910.151746X-RAY DIFFRACTION99.837
3.964-4.1780.202950.1481661X-RAY DIFFRACTION99.8862
4.178-4.4310.2850.151553X-RAY DIFFRACTION99.939
4.431-4.7370.151670.1341482X-RAY DIFFRACTION99.7424
4.737-5.1160.192810.1431354X-RAY DIFFRACTION99.9304
5.116-5.6030.207690.1561270X-RAY DIFFRACTION99.8509
5.603-6.2630.203610.1951144X-RAY DIFFRACTION99.8343
6.263-7.230.268570.2141018X-RAY DIFFRACTION100
7.23-8.850.222420.19871X-RAY DIFFRACTION99.6725
8.85-12.4920.215340.197680X-RAY DIFFRACTION99.8601
12.492-48.4410.233190.307374X-RAY DIFFRACTION96.5602

+
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