[English] 日本語
Yorodumi
- PDB-8i12: InuAMN8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i12
TitleInuAMN8
ComponentsGlycosyl hydrolase family 32 exo-inulinase
KeywordsHYDROLASE / Cold-active / NaCl-tolerant / exo-inulinase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glycosyl hydrolase family 32 exo-inulinase
Similarity search - Component
Biological speciesArthrobacter sp. MN8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsZhou, J.P. / Cen, X.L. / He, L.M. / Zhang, R. / Huang, Z.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cold-active and NaCl-tolerant exo-inulinase InuAMN8.
Authors: Cen, X.L. / He, L.M. / Zhang, R. / Huang, Z.X. / Zhou, J.P.
History
DepositionJan 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl hydrolase family 32 exo-inulinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7336
Polymers57,2451
Non-polymers4895
Water11,998666
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.630, 79.220, 94.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Glycosyl hydrolase family 32 exo-inulinase


Mass: 57244.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. MN8 (bacteria) / Gene: inuA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0F6MV26
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: JCSG4-60 0.1 M HEPES pH 6.5, 30% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.36→94.57 Å / Num. obs: 99430 / % possible obs: 99.3 % / Redundancy: 12.2 % / Biso Wilson estimate: 7.89 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.7
Reflection shellResolution: 1.36→1.39 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 9000 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
DIALS3.7.2data reduction
DIALS3.7.2data scaling
PHENIX10.1-2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→48.64 Å / SU ML: 0.1035 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.5827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1494 2000 2.01 %
Rwork0.1243 97289 -
obs0.1248 99289 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.73 Å2
Refinement stepCycle: LAST / Resolution: 1.36→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 32 666 4489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01284059
X-RAY DIFFRACTIONf_angle_d1.38565546
X-RAY DIFFRACTIONf_chiral_restr0.2016574
X-RAY DIFFRACTIONf_plane_restr0.0098742
X-RAY DIFFRACTIONf_dihedral_angle_d21.9231449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.15291300.1036305X-RAY DIFFRACTION90.98
1.39-1.430.16241410.10296890X-RAY DIFFRACTION99.36
1.43-1.470.14051410.10096893X-RAY DIFFRACTION99.97
1.47-1.520.14561440.09696942X-RAY DIFFRACTION99.99
1.52-1.570.14271420.0936947X-RAY DIFFRACTION99.99
1.57-1.640.12561420.09836940X-RAY DIFFRACTION100
1.64-1.710.15591440.10676976X-RAY DIFFRACTION99.99
1.71-1.80.14291440.11236964X-RAY DIFFRACTION99.99
1.8-1.920.14091430.11666983X-RAY DIFFRACTION100
1.92-2.060.15221440.11976991X-RAY DIFFRACTION99.97
2.06-2.270.13121440.12067012X-RAY DIFFRACTION99.99
2.27-2.60.15011440.13997058X-RAY DIFFRACTION99.99
2.6-3.280.16611470.14467123X-RAY DIFFRACTION99.96
3.28-3.560.15541500.14587265X-RAY DIFFRACTION98.54

+
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