[English] 日本語
Yorodumi
- PDB-8g5w: Structure of the Class II Fructose-1,6-Bisphophatase from Francis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g5w
TitleStructure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis complexed with native metal cofactor Mn++
ComponentsFructose-1,6-bisphosphataseFructose 1,6-bisphosphatase
KeywordsHYDROLASE / class II FBPases / fructose-1 / 6-bisphosphatase / Francisella tularensis / Mycobacterium tuberculosis / gluconeogenesis / antibiotic targets / HYDROLASE-PRODUCT complex
Function / homologyFructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded / glycerol metabolic process / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / metal ion binding / : / Fructose-1,6-bisphosphatase
Function and homology information
Biological speciesFrancisella cf. tularensis subsp. novicida 3523 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAbad-Zapatero, C. / Selezneva, A.I.
Funding support2items
OrganizationGrant numberCountry
Other privatePotts Memorial Foundation G3541
Other privateChicago Biomedical Consortium 084679-00001
CitationJournal: Plos One / Year: 2023
Title: New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class.
Authors: Selezneva, A.I. / Harding, L.N.M. / Gutka, H.J. / Movahedzadeh, F. / Abad-Zapatero, C.
History
DepositionFeb 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase
B: Fructose-1,6-bisphosphatase
C: Fructose-1,6-bisphosphatase
D: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,99026
Polymers148,1124
Non-polymers1,87722
Water10,052558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complete tetramer in the a.u.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.845, 75.879, 77.616
Angle α, β, γ (deg.)67.831, 68.136, 76.372
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
Fructose-1,6-bisphosphatase / Fructose 1,6-bisphosphatase


Mass: 37028.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella cf. tularensis subsp. novicida 3523 (bacteria)
Gene: glpX, FNC33_05530, FNC42_07040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZJY0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Hampton Research PEG/Ion2 #14 8% Tacsimate 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2022
RadiationMonochromator: Sillicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 83239 / % possible obs: 98 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Rsym value: 0.086 / Net I/σ(I): 24.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4064 / CC1/2: 0.808 / Rpim(I) all: 0.339 / Rrim(I) all: 0.653 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.37 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.4066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2045 4080 4.96 %
Rwork0.1607 78258 -
obs0.1628 82338 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.77 Å2
Refinement stepCycle: LAST / Resolution: 2→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9682 0 112 559 10353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01519874
X-RAY DIFFRACTIONf_angle_d1.424613285
X-RAY DIFFRACTIONf_chiral_restr0.06571553
X-RAY DIFFRACTIONf_plane_restr0.00861728
X-RAY DIFFRACTIONf_dihedral_angle_d18.19011424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.24321430.1952573X-RAY DIFFRACTION96.9
2.02-2.050.27161250.19352751X-RAY DIFFRACTION96.93
2.05-2.070.2411700.18642592X-RAY DIFFRACTION96.91
2.07-2.10.22611580.19042664X-RAY DIFFRACTION96.91
2.1-2.130.26351430.18392692X-RAY DIFFRACTION97.49
2.13-2.160.25281450.18452669X-RAY DIFFRACTION96.83
2.16-2.190.24471260.18432688X-RAY DIFFRACTION97.47
2.19-2.230.2431610.18092665X-RAY DIFFRACTION97.28
2.23-2.260.26661430.18342674X-RAY DIFFRACTION97.61
2.26-2.30.23941350.17832732X-RAY DIFFRACTION97.45
2.3-2.340.22861300.16812671X-RAY DIFFRACTION97.49
2.34-2.390.21311360.16182689X-RAY DIFFRACTION97.78
2.39-2.440.22691420.16192725X-RAY DIFFRACTION97.65
2.44-2.490.2231410.15562677X-RAY DIFFRACTION97.95
2.49-2.550.20851450.16232705X-RAY DIFFRACTION97.94
2.55-2.610.22381410.1622687X-RAY DIFFRACTION97.89
2.61-2.680.23271350.17082702X-RAY DIFFRACTION98.2
2.68-2.760.25851430.16622725X-RAY DIFFRACTION98.25
2.76-2.850.21831310.16722685X-RAY DIFFRACTION98.19
2.85-2.950.19591480.16462705X-RAY DIFFRACTION98.45
2.95-3.070.22831420.17562737X-RAY DIFFRACTION98.49
3.07-3.210.25031650.17252693X-RAY DIFFRACTION98.59
3.21-3.380.20091560.16112692X-RAY DIFFRACTION98.72
3.38-3.590.19681450.15322726X-RAY DIFFRACTION98.97
3.59-3.870.17241260.14732738X-RAY DIFFRACTION98.9
3.87-4.260.18391160.1372774X-RAY DIFFRACTION99.21
4.26-4.870.14921260.12722734X-RAY DIFFRACTION99.24
4.87-6.140.17461270.15952755X-RAY DIFFRACTION99.41
6.14-37.370.15511360.16652738X-RAY DIFFRACTION98.9

+
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