[English] 日本語
Yorodumi
- PDB-7js3: Structure of the Class II Fructose-1,6-Bisphophatase from Francis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7js3
TitleStructure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis
ComponentsFructose-1,6-bisphosphatase
KeywordsHYDROLASE / Class II FBPase / Gluconeogenesis / F. tularensis / antibacterial
Function / homology
Function and homology information


glycerol metabolic process / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / metal ion binding / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAbad-Zapatero, C. / Wolf, N.M. / Movahedzadeh, F. / Gutka, H. / Selezneva, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Potts Memorial FoundationG3541 United States
Chicago Biomedical Consortium084679-00001 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis.
Authors: Selezneva, A.I. / Gutka, H.J. / Wolf, N.M. / Qurratulain, F. / Movahedzadeh, F. / Abad-Zapatero, C.
History
DepositionAug 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 30, 2021Group: Data collection / Category: pdbx_reflns_twin
Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)148,76214
Polymers148,1124
Non-polymers65010
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, There is a full tetramer in the crystal assymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-29 kcal/mol
Surface area45820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.296, 100.169, 92.021
Angle α, β, γ (deg.)90.000, 90.003, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Fructose-1,6-bisphosphatase


Mass: 37028.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: glpX, EGT35_01410, FNC33_05530, FNC42_07040 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2ZJY0, UniProt: Q5NEJ8*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.4 Å3/Da / Density % sol: 51.23 % / Description: Prismatic needles
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 20 mM Tricine pH 7.8, 50 mM KCl, 1 mM MgCl2, 0.1 mM DTT, 15% glycerol; Composition of reservoir solution 0.2 M sodium formate, 20% PEG 3350; Volume and ratio of drop 22.4 uL (1:1) Volume of reservoir (ul) 100

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.92456 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2017
RadiationMonochromator: Si (1111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92456 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5676
pseudo-merohedral11-h,-k,l20.4324
ReflectionResolution: 2.4→40 Å / Num. obs: 53682 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 42.9 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.106 / Rsym value: 0.106 / Net I/σ(I): 24.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2620 / CC1/2: 0.673 / Rpim(I) all: 0.276 / Rrim(I) all: 0.531 / Rsym value: 0.531 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.16-3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ayu

6ayu


Resolution: 2.4→38.11 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.495 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1 / ESU R: 0.074 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2732 5.113 %2732
Rwork0.1534 50918 --
obs0.155 53662 98.747 %-
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: 48.033 Å2
Baniso -1Baniso -2Baniso -3
1--5.067 Å20 Å2-3.658 Å2
2---0.204 Å20 Å2
3---5.271 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9624 0 40 172 9836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139785
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179412
X-RAY DIFFRACTIONr_angle_refined_deg1.51.63113176
X-RAY DIFFRACTIONr_angle_other_deg1.6051.58321763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.495.141317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76422.759464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.094151708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3731563
X-RAY DIFFRACTIONr_chiral_restr0.0680.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021894
X-RAY DIFFRACTIONr_nbd_refined0.2080.22344
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.210095
X-RAY DIFFRACTIONr_nbtor_refined0.170.24863
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.25343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.2347
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1380.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.224
X-RAY DIFFRACTIONr_nbd_other0.3430.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1020.21
X-RAY DIFFRACTIONr_mcbond_it3.7475.0975200
X-RAY DIFFRACTIONr_mcbond_other3.7465.0965199
X-RAY DIFFRACTIONr_mcangle_it5.4297.6446494
X-RAY DIFFRACTIONr_mcangle_other5.4297.6456495
X-RAY DIFFRACTIONr_scbond_it3.8735.3384585
X-RAY DIFFRACTIONr_scbond_other3.8735.3384586
X-RAY DIFFRACTIONr_scangle_it5.5037.916680
X-RAY DIFFRACTIONr_scangle_other5.5037.9116681
X-RAY DIFFRACTIONr_lrange_it7.69262.53210858
X-RAY DIFFRACTIONr_lrange_other7.69262.53610859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.2451820.2023647X-RAY DIFFRACTION95.5101
2.46-2.5280.2561930.1993621X-RAY DIFFRACTION98.8339
2.528-2.6010.2641950.2023559X-RAY DIFFRACTION98.7895
2.601-2.6810.2862020.1923447X-RAY DIFFRACTION98.9425
2.681-2.7690.2212060.1973325X-RAY DIFFRACTION99.0185
2.769-2.8660.2181690.1713259X-RAY DIFFRACTION99.1898
2.866-2.9740.2191700.1793154X-RAY DIFFRACTION99.3425
2.974-3.0950.231730.1792994X-RAY DIFFRACTION98.9688
3.095-3.2330.2091890.1772887X-RAY DIFFRACTION98.9067
3.233-3.390.2271110.1712789X-RAY DIFFRACTION98.8749
3.39-3.5740.2181210.1652645X-RAY DIFFRACTION98.7857
3.574-3.790.181410.1572490X-RAY DIFFRACTION98.7613
3.79-4.0510.1881100.1352366X-RAY DIFFRACTION99.0796
4.051-4.3750.1441200.1172199X-RAY DIFFRACTION98.9757
4.375-4.7920.1281090.1052002X-RAY DIFFRACTION98.9222
4.792-5.3550.124910.1321840X-RAY DIFFRACTION99.6388
5.355-6.180.2191010.1571634X-RAY DIFFRACTION99.7126
6.18-7.5610.178720.1371384X-RAY DIFFRACTION99.9314
7.561-10.6570.179500.1121091X-RAY DIFFRACTION99.5637
10.657-38.110.2451820.202585X-RAY DIFFRACTION95.2672

+
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