[English] 日本語
Yorodumi
- PDB-1xfb: Human Brain Fructose 1,6-(bis)phosphate Aldolase (C isozyme) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xfb
TitleHuman Brain Fructose 1,6-(bis)phosphate Aldolase (C isozyme)
ComponentsAldolase C
KeywordsLYASE / isozyme specificity / structural enzymology / protein-protein interactions / isozyme specific residues / structure/function
Function / homology
Function and homology information


neutrophil degranulation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / Gluconeogenesis / canonical glycolysis / Glycolysis / epithelial cell differentiation / cytoskeletal protein binding ...neutrophil degranulation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / Gluconeogenesis / canonical glycolysis / Glycolysis / epithelial cell differentiation / cytoskeletal protein binding / gluconeogenesis / glycolytic process / tertiary granule lumen / secretory granule lumen / ficolin-1-rich granule lumen / cytoskeleton / Neutrophil degranulation / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArakaki, T.L. / Pezza, J.A. / Cronin, M.A. / Hopkins, C.E. / Zimmer, D.B. / Tolan, D.R. / Allen, K.N.
CitationJournal: Protein Sci. / Year: 2004
Title: Structure of human brain fructose 1,6-(bis)phosphate aldolase: linking isozyme structure with function
Authors: Arakaki, T.L. / Pezza, J.A. / Cronin, M.A. / Hopkins, C.E. / Zimmer, D.B. / Tolan, D.R. / Allen, K.N.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: Aldolase C
B: Aldolase C
C: Aldolase C
D: Aldolase C
E: Aldolase C
F: Aldolase C
G: Aldolase C
H: Aldolase C
I: Aldolase C
J: Aldolase C
K: Aldolase C
L: Aldolase C


Theoretical massNumber of molelcules
Total (without water)475,40412
Polymers475,40412
Non-polymers00
Water0
1
A: Aldolase C
B: Aldolase C
C: Aldolase C
D: Aldolase C


Theoretical massNumber of molelcules
Total (without water)158,4684
Polymers158,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Aldolase C
F: Aldolase C
G: Aldolase C
H: Aldolase C


Theoretical massNumber of molelcules
Total (without water)158,4684
Polymers158,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Aldolase C
J: Aldolase C
K: Aldolase C
L: Aldolase C


Theoretical massNumber of molelcules
Total (without water)158,4684
Polymers158,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.872, 121.986, 129.517
Angle α, β, γ (deg.)107.96, 108.58, 97.39
Int Tables number1
Space group name H-MP1
DetailsTetramer of molecules A, B, C, D / Tetramer of molecules E, F, G, H / Tetramer of molecules I, J, K, L

-
Components

#1: Protein
Aldolase C / Fructose 1 / 6-(bis)phosphate Aldolase


Mass: 39616.973 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P09972, fructose-bisphosphate aldolase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Calcium Acetate, Tris, glucose, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2003 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→79.24 Å / Num. all: 89550 / Num. obs: 89550 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 27 / Limit h min: -29 / Limit k max: 41 / Limit k min: -29 / Limit l max: 46 / Limit l min: 0 / Observed criterion F max: 1989158.51 / Observed criterion F min: 6.4 / Rsym value: 0.097 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.15 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.34 / % possible all: 95.5

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1J4E

1j4e


Resolution: 3→79.24 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 8700 10 %random
Rwork0.255 ---
all0.257 89706 --
obs0.257 87177 97.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 30.8274 Å2 / ksol: 0.370575 e/Å3
Displacement parametersBiso max: 99.51 Å2 / Biso mean: 35.37 Å2 / Biso min: 0.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å27.22 Å22.25 Å2
2--9.79 Å28.67 Å2
3----6.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.67 Å
Luzzati d res high-3
Refinement stepCycle: LAST / Resolution: 3→79.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31476 0 0 0 31476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg21.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3-3.140.382111810.40.38596020.011112201072095.5
3.14-3.30.3310289.50.33997540.01112191078296.1
3.3-3.510.313111310.20.397610.009112731087496.5
3.51-3.780.28110549.70.27398000.009111801085497.1
3.78-4.160.25110410.10.2498250.008112081092997.5
4.16-4.760.22210749.70.20799540.007112591102897.9
4.76-60.2181098100.21799150.007112081101398.3
6-79.240.212111110.10.20998660.006112071097797.9
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

+
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