[English] 日本語
Yorodumi
- PDB-1fbt: THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fbt
TitleTHE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE
ComponentsFRUCTOSE-2,6-BISPHOSPHATASE
KeywordsHYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSFERASE / KINASE
Function / homology
Function and homology information


positive regulation of glycolytic process through fructose-6-phosphate / 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / carbohydrate phosphorylation / fructose-6-phosphate binding ...positive regulation of glycolytic process through fructose-6-phosphate / 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / carbohydrate phosphorylation / fructose-6-phosphate binding / fructose metabolic process / response to glucagon / response to starvation / negative regulation of glycolytic process through fructose-6-phosphate / response to cAMP / animal organ regeneration / response to glucocorticoid / response to insulin / kinase binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily ...Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLee, Y.-H. / Ogata, C. / Pflugrath, J.W. / Levitt, D.G. / Sarma, R. / Banaszak, L.J. / Pilkis, S.J.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of the rat liver fructose-2,6-bisphosphatase based on selenomethionine multiwavelength anomalous dispersion phases.
Authors: Lee, Y.H. / Ogata, C. / Pflugrath, J.W. / Levitt, D.G. / Sarma, R. / Banaszak, L.J. / Pilkis, S.J.
#1: Journal: Annu.Rev.Biochem. / Year: 1995
Title: 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase: A Metabolic Signaling Enzyme
Authors: Pilkis, S.J. / Claus, T.H. / Kurland, I.J. / Lange, A.J.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Preliminary X-Ray Analysis of a Truncated Form of Recombinant Fructose-2,6-Bisphosphatase
Authors: Lee, Y.H. / Lin, K. / Okar, D. / Alfano, N.L. / Sarma, R. / Pflugrath, J.W. / Pilkis, S.J.
History
DepositionMar 8, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRUCTOSE-2,6-BISPHOSPHATASE
B: FRUCTOSE-2,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6614
Polymers44,4712
Non-polymers1902
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.400, 56.600, 93.700
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.0119, -0.0012), (-0.0112, 0.89239, 0.45113), (-0.0432, 0.45111, -0.8925)
Vector: 36.2697, -10.733, 45.7646)

-
Components

#1: Protein FRUCTOSE-2,6-BISPHOSPHATASE / D-FRUCTOSE-2 / 6-BISPHOSPHATE 2-PHOSPHOHYDROLASE


Mass: 22235.746 Da / Num. of mol.: 2 / Mutation: 30 AMINO ACIDS DELETED FROM THE C-TERMINAL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: A CODING REGION WHICH COVERS / Organ: LIVER / Plasmid: PET3A
Gene (production host): A CODING REGION WHICH COVERS FRUCTOSE-2,6-BISPHOSPHATASE DOMAIN (RESIDUES 251-440) OF THE RAT LIVER 6-PF-2-K/FRU-2,6-P2ASE (RESIDUES 1-470)
Production host: Escherichia coli (E. coli) / Strain (production host): DL41 DE3
References: UniProt: P07953, fructose-2,6-bisphosphate 2-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE: FRU-2,6-BISPHOSPHATASE. THE FRU-2,6-BISPHOSPHATASE IS C-TERMINAL HALF (RESIDUE 251- ...COMPND MOLECULE: FRU-2,6-BISPHOSPHATASE. THE FRU-2,6-BISPHOSPHATASE IS C-TERMINAL HALF (RESIDUE 251-470) OF THE BIFUNCTIONAL 6-PHOSPHOFRUCTO-2-KINASE/FRU-2,6-BISPHOSPHATASE (470 AMINO ACIDS). THE STRUCTURE PRESENTED HERE IS FROM THE CLONE WHICH COVERS THE CORE BISPHOSPHATASE DOMAIN (RESIDUES 251-440) OF THE BIFUNCTIONAL ENZYME. THE STRUCTURE WAS DETERMINED BY MAD PHASING WHERE THE MAD DATA FROM THE SELENOMETHIONINE-LABELLED BISPHOSPHATASE WERE TREATED FOR MIR-STYLE PHASE CALCULATION. A COMPETITIVE INHIBITOR, PHOSPHATE, WAS USED FOR THE CRYSTALLIZATION BUFFER. THE PRESENCE OF PI IN THE PROTEIN STRUCTURE WAS USED TO IDENTIFY THE ACTIVE SITE.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 52 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
215 %PEG40001drop
35 mMsodium phosphate1drop
40.5 mMdithiothreitol1drop
52.5 %glycerol1drop
630 %PEG40001reservoir
710 mMsodium phosphate1reservoir
81 mMdithiothreitol1reservoir
95 %glycerol1reservoir
10water1drop

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionNum. obs: 32129 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. obs: 15137

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2→20 Å / σ(F): 2
RfactorNum. reflection
Rfree0.278 -
Rwork0.218 -
obs0.218 27821
Displacement parametersBiso mean: 27.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 10 161 3265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.597
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.561
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Rfactor obs: 0.208 / Rfactor Rfree: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.561

+
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