[English] 日本語
Yorodumi
- PDB-8hsn: Crystal structure of DFA I-forming Inulin Lyase from Streptomyces... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hsn
TitleCrystal structure of DFA I-forming Inulin Lyase from Streptomyces peucetius subsp. caesius ATCC 27952
ComponentsFructotransferase
KeywordsLYASE / right-handed beta-helix protein / DFA I-forming inulin lyase
Function / homology
Function and homology information


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
Similarity search - Domain/homology
PHOSPHONATE / DI(HYDROXYETHYL)ETHER / Fructotransferase
Similarity search - Component
Biological speciesStreptomyces peucetius subsp. caesius ATCC 27952 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsCheng, M. / Rao, Y.J. / Mu, W.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31922073 China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural Insights into the Catalytic Cycle of Inulin Fructotransferase: From Substrate Anchoring to Product Releasing.
Authors: Cheng, M. / Hou, X. / Huang, Z. / Chen, Z. / Ni, D. / Zhang, W. / Rao, Y. / Mu, W.
History
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructotransferase
B: Fructotransferase
C: Fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,52853
Polymers128,2583
Non-polymers4,27050
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25190 Å2
ΔGint2 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.680, 102.510, 132.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Fructotransferase / inulin lyase [DFA I-forming]


Mass: 42752.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius subsp. caesius ATCC 27952 (bacteria)
Gene: CGZ69_03210 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2D3U3Z1, inulin fructotransferase (DFA-I-forming)

-
Non-polymers , 6 types, 603 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-2PO / PHOSPHONATE


Mass: 79.980 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO3P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate, 12% Polyethylene glycol 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.69→47.81 Å / Num. obs: 147518 / % possible obs: 99 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 22.8
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 14488 / CC1/2: 0.969 / Rrim(I) all: 0.374

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSBUILT=20220220data reduction
XSCALEBUILT=20220220data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→47.81 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1512 1993 1.35 %
Rwork0.1368 --
obs0.137 147498 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8882 0 275 553 9710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099330
X-RAY DIFFRACTIONf_angle_d1.04612627
X-RAY DIFFRACTIONf_dihedral_angle_d11.8531345
X-RAY DIFFRACTIONf_chiral_restr0.0641464
X-RAY DIFFRACTIONf_plane_restr0.0081629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.16951530.143810178X-RAY DIFFRACTION98
1.73-1.780.1671250.132710249X-RAY DIFFRACTION98
1.78-1.830.14221440.133410212X-RAY DIFFRACTION98
1.83-1.890.1541450.135610269X-RAY DIFFRACTION99
1.89-1.960.17841440.132110260X-RAY DIFFRACTION99
1.96-2.040.14481330.127410294X-RAY DIFFRACTION99
2.04-2.130.1471440.130210348X-RAY DIFFRACTION99
2.13-2.240.16971290.133110350X-RAY DIFFRACTION99
2.24-2.380.14241440.133110384X-RAY DIFFRACTION99
2.38-2.570.16411410.132610444X-RAY DIFFRACTION99
2.57-2.820.15211460.133210435X-RAY DIFFRACTION99
2.82-3.230.13341510.140310540X-RAY DIFFRACTION100
3.23-4.070.14431410.138410613X-RAY DIFFRACTION100
4.07-47.810.15161530.149110929X-RAY DIFFRACTION100

+
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