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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tip
TitleTHE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE
ComponentsPHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE
KeywordsHYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSFERASE / KINASE / ATP-BINDING / PHOSPHORYLATION / ALTERNATIVE SPLICING / MULTIGENE FAMILY
Function / homology
Function and homology information


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 / fructose-6-phosphate binding / carbohydrate phosphorylation / fructose metabolic process ...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 / fructose-6-phosphate binding / carbohydrate phosphorylation / fructose metabolic process / response to glucagon / negative regulation of glycolytic process through fructose-6-phosphate / response to starvation / animal organ regeneration / response to glucocorticoid / response to cAMP / 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
6-O-phosphono-beta-D-fructofuranose / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLee, Y.-H. / Olson, T.W. / Ogata, C.M. / Levitt, D.G. / Banaszak, L.J. / Lange, A.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of a trapped phosphoenzyme during a catalytic reaction.
Authors: Lee, Y.H. / Olson, T.W. / Ogata, C.M. / Levitt, D.G. / Banaszak, L.J. / Lange, A.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
DepositionMay 28, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE
B: PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0374
Polymers44,5172
Non-polymers5202
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.230, 56.520, 90.900
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999546, -0.029783, -0.004615), (-0.028588, 0.888466, 0.458052), (-0.009541, 0.457976, -0.888914)
Vector: 36.4465, -10.40655, 46.48539)

-
Components

#1: Protein PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE / D-FRUCTOSE-2 / 6-BISPHOSPHATE 2-PHOSPHOHYDROLASE


Mass: 22258.334 Da / Num. of mol.: 2 / Mutation: 30 C-TERMINAL AMINO ACIDS DELETED
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: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA COMPETITIVE INHIBITOR, PHOSPHATE, WAS USED FOR THE CRYSTALLIZATION BUFFER. THE PRESENCE OF PI IN ...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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 52 % / Description: NUMBER OF CRYSTALS 1.
Crystal growDetails: A CATALYTIC PHOSPHOSENZYME INTERMEDIATE STATE OF THE BISPHOSPHATASE WAS PREPARED BY SOAKING OF THE NATIVE CRYSTAL OF THE PROTEIN AND TRAPPED USING THE CRYOGENIC DEVICE. A 2.2 ANGSTROM ...Details: A CATALYTIC PHOSPHOSENZYME INTERMEDIATE STATE OF THE BISPHOSPHATASE WAS PREPARED BY SOAKING OF THE NATIVE CRYSTAL OF THE PROTEIN AND TRAPPED USING THE CRYOGENIC DEVICE. A 2.2 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE INTERMEDIATE WAS DETERMINED. A PHOSPHORYLATED CATALYTIC HISTIDINE WAS VISUALIZED ALONG WITH THE FIRST PRODUCT, FRUCTOSE-6 - PHOSPHATE, AND THE CATALYTIC WATER, SHOWING THE COMPREHENSIVE GEOMETRY OF A TRIGONAL BI-PYRAMIDAL STRUCTURE.
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Lee, Y.H., (1996) Biochemistry, 35, 6010.
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: X4A / Wavelength: 1.02
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 5, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionNum. obs: 20142 / % possible obs: 78.3 % / Observed criterion σ(I): 3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.033

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.2→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.286 -
Rwork0.204 -
obs0.204 20142
Displacement parametersBiso mean: 27.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 32 284 3434
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.942 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.466
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://pdbjlvh1.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