[English] 日本語
Yorodumi
- PDB-1spi: CRYSTAL STRUCTURE OF SPINACH CHLOROPLAST FRUCTOSE-1,6-BISPHOSPHAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1spi
TitleCRYSTAL STRUCTURE OF SPINACH CHLOROPLAST FRUCTOSE-1,6-BISPHOSPHATASE AT 2.8 ANGSTROMS RESOLUTION
ComponentsFRUCTOSE 1,6-BISPHOSPHATASE
KeywordsHYDROLASE (PHOSPHORIC MONOESTER)
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / reductive pentose-phosphate cycle / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / fructose 6-phosphate metabolic process / chloroplast / gluconeogenesis / metal ion binding ...sucrose biosynthetic process / fructose-bisphosphatase / reductive pentose-phosphate cycle / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / fructose 6-phosphate metabolic process / chloroplast / gluconeogenesis / metal ion binding / 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, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsVilleret, V. / Huang, S. / Zhang, Y. / Xue, Y. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure of spinach chloroplast fructose-1,6-bisphosphatase at 2.8 A resolution.
Authors: Villeret, V. / Huang, S. / Zhang, Y. / Xue, Y. / Lipscomb, W.N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Toward a Mechanism for the Allosteric Transition of Pig Kidney Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.-Y. / Huang, S. / Lipscomb, W.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal Structure of Fructose-1,6-Bisphosphatase Complexed with Fructose 2,6-Bisphosphate, AMP and Zn2+ at 2.0 Angstroms Resolution. Aspects of Synergism between Inhibitors
Authors: Xue, Y. / Huang, S. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1993
Title: Crystallographic Studies of the Catalytic Mechanism of the Neutral Form of Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.-Y. / Huang, S. / Ke, H. / Lipscomb, W.N.
History
DepositionDec 14, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
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


Theoretical massNumber of molelcules
Total (without water)156,7254
Polymers156,7254
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-70 kcal/mol
Surface area56010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.100, 85.700, 105.800
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
FRUCTOSE 1,6-BISPHOSPHATASE


Mass: 39181.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / References: UniProt: P22418, fructose-bisphosphatase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growDetails: COMPND PH 5.2.
Crystal grow
*PLUS
pH: 5.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlenzyme11
280 mM12NaAc
30.3 mMammonium sulfate12
40.3 mMNa citrate12
52 %(w/v)PEG145012
62 %(w/v)PEG335012
74 mM12NaN3
80.2 mMEDTA12
90.3 mMoctylphenoxypoly(ethoxyethanol)12

-
Data collection

ReflectionNum. obs: 29281 / % possible obs: 83.3 %
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.106

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.203 / Rfactor obs: 0.203 / σ(F): 2
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12358 0 0 0 12358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

+
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