[English] 日本語
Yorodumi
- PDB-5et5: Human muscle fructose-1,6-bisphosphatase in active R-state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5et5
TitleHuman muscle fructose-1,6-bisphosphatase in active R-state
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle / FBPase / R-state / Leucine lock / Asp187
Function / homology
Function and homology information


fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome ...fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase isozyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsBarciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/09/B/NZ1/01081 Poland
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure.
Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Jaskolski, M. / Rakus, D. / Dzugaj, A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2011
Title: Structure of E69Q mutant of human muscle fructose-1,6-bisphosphatase.
Authors: Zarzycki, M. / Kolodziejczyk, R. / Maciaszczyk-Dziubinska, E. / Wysocki, R. / Jaskolski, M. / Dzugaj, A.
#2: Journal: PLoS ONE / Year: 2013
Title: Crystal structures of human muscle fructose-1,6-bisphosphatase: novel quaternary states, enhanced AMP affinity, and allosteric signal transmission pathway.
Authors: Shi, R. / Chen, Z.Y. / Zhu, D.W. / Li, C. / Shan, Y. / Xu, G. / Lin, S.X.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 isozyme 2


Theoretical massNumber of molelcules
Total (without water)36,6671
Polymers36,6671
Non-polymers00
Water2,396133
1
A: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2


Theoretical massNumber of molelcules
Total (without water)146,6684
Polymers146,6684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9880 Å2
ΔGint-62 kcal/mol
Surface area45250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.564, 72.564, 235.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21A-523-

HOH

-
Components

#1: Protein Fructose-1,6-bisphosphatase isozyme 2 / FBPase 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 2 / Muscle FBPase


Mass: 36666.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: skeletal muscle / Gene: FBP2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): C100 / References: UniProt: O00757, fructose-bisphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10mM magnesium chloride, 2M sodium chloride, 10%PEG6000, 10mM Tris
PH range: 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→36.28 Å / Num. all: 37062 / Num. obs: 37062 / % possible obs: 99.8 % / Redundancy: 13.03 % / Biso Wilson estimate: 24.92 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.89
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 13.18 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 3.08 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IFA

3ifa


Resolution: 1.67→36.28 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / Phase error: 23.23 / Stereochemistry target values: ENGH & HUBER / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1001 2.7 %Random selection
Rwork0.1933 ---
obs0.194 37060 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.09 Å2
Refinement stepCycle: LAST / Resolution: 1.67→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 0 133 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192217
X-RAY DIFFRACTIONf_angle_d1.7912996
X-RAY DIFFRACTIONf_dihedral_angle_d14.665825
X-RAY DIFFRACTIONf_chiral_restr0.094356
X-RAY DIFFRACTIONf_plane_restr0.01374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6689-1.75680.27231390.23735026X-RAY DIFFRACTION99
1.7568-1.86690.27281420.22485105X-RAY DIFFRACTION100
1.8669-2.0110.27481400.23765059X-RAY DIFFRACTION100
2.011-2.21340.22651420.19295103X-RAY DIFFRACTION100
2.2134-2.53360.25711420.20335131X-RAY DIFFRACTION100
2.5336-3.19180.21551450.19895202X-RAY DIFFRACTION100
3.1918-36.29060.18791510.1745433X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92450.3482-0.48195.266-3.96433.79610.1902-0.0526-0.06330.77-0.1883-0.399-0.60850.1511-0.0160.3643-0.1137-0.07840.2555-0.01590.4677-12.25085.30569.6408
24.1742-0.4765-1.55884.19843.60384.68040.0749-0.4289-0.06040.81770.01-1.00460.1640.3403-0.22150.5909-0.1768-0.38370.34940.08020.6309-6.7475-7.483120.1749
33.60130.33390.11361.12990.56382.95860.0769-0.48250.40911.3058-0.1731-0.8445-0.30190.186-0.0990.7959-0.1246-0.20010.2527-0.00870.3617-15.8197-4.545924.8106
46.5433-0.4889-2.92632.3080.88575.97980.2171-0.81260.38040.9199-0.0096-0.1255-0.33530.0117-0.10260.532-0.0384-0.00990.219-0.02650.2806-24.6993-3.896822.5114
51.3890.45480.26943.92470.25441.01320.00740.09090.0889-0.0003-0.03070.0882-0.034-0.01360.02580.1147-0.0240.02030.17450.03030.1512-27.4168-12.77552.8497
62.37750.32750.36143.54130.7022.37320.0929-0.12150.04260.5263-0.0070.20310.1031-0.0908-0.06440.2238-0.04980.0530.14160.01220.1832-30.3888-14.351713.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 247 )
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 331 )

+
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