[English] 日本語
Yorodumi
- PDB-1qo5: Fructose 1,6-bisphosphate Aldolase from Human Liver Tissue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qo5
TitleFructose 1,6-bisphosphate Aldolase from Human Liver Tissue
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE B
KeywordsLYASE / ALDOLASE / TIM BARREL / GLYCOLYTIC ENZYME
Function / homology
Function and homology information


Hereditary fructose intolerance / fructose-1-phosphate aldolase activity / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / vacuolar proton-transporting V-type ATPase complex assembly / fructose binding / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis ...Hereditary fructose intolerance / fructose-1-phosphate aldolase activity / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / vacuolar proton-transporting V-type ATPase complex assembly / fructose binding / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / negative regulation of pentose-phosphate shunt / Glycolysis / microtubule organizing center / cytoskeletal protein binding / glycolytic process / gluconeogenesis / centriolar satellite / ATPase binding / molecular adaptor activity / extracellular exosome / identical protein binding / 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 B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDalby, A.R. / Littlechild, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The Structure of Human Liver Fructose-1,6-Bisphosphate Aldolase
Authors: Dalby, A.R. / Tolan, D.R. / Littlechild, J.A.
History
DepositionNov 3, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE B
B: FRUCTOSE-BISPHOSPHATE ALDOLASE B
C: FRUCTOSE-BISPHOSPHATE ALDOLASE B
D: FRUCTOSE-BISPHOSPHATE ALDOLASE B
E: FRUCTOSE-BISPHOSPHATE ALDOLASE B
F: FRUCTOSE-BISPHOSPHATE ALDOLASE B
G: FRUCTOSE-BISPHOSPHATE ALDOLASE B
H: FRUCTOSE-BISPHOSPHATE ALDOLASE B
I: FRUCTOSE-BISPHOSPHATE ALDOLASE B
J: FRUCTOSE-BISPHOSPHATE ALDOLASE B
K: FRUCTOSE-BISPHOSPHATE ALDOLASE B
L: FRUCTOSE-BISPHOSPHATE ALDOLASE B
M: FRUCTOSE-BISPHOSPHATE ALDOLASE B
N: FRUCTOSE-BISPHOSPHATE ALDOLASE B
O: FRUCTOSE-BISPHOSPHATE ALDOLASE B
P: FRUCTOSE-BISPHOSPHATE ALDOLASE B
Q: FRUCTOSE-BISPHOSPHATE ALDOLASE B
R: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,43933
Polymers708,99818
Non-polymers1,44115
Water21,0601169
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE B
B: FRUCTOSE-BISPHOSPHATE ALDOLASE B
C: FRUCTOSE-BISPHOSPHATE ALDOLASE B
D: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8437
Polymers157,5554
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint2.4 kcal/mol
Surface area59920 Å2
MethodPQS
2
E: FRUCTOSE-BISPHOSPHATE ALDOLASE B
F: FRUCTOSE-BISPHOSPHATE ALDOLASE B
G: FRUCTOSE-BISPHOSPHATE ALDOLASE B
H: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9398
Polymers157,5554
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-9.6 kcal/mol
Surface area60140 Å2
MethodPQS
3
I: FRUCTOSE-BISPHOSPHATE ALDOLASE B
J: FRUCTOSE-BISPHOSPHATE ALDOLASE B
K: FRUCTOSE-BISPHOSPHATE ALDOLASE B
L: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7476
Polymers157,5554
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-57.4 kcal/mol
Surface area59540 Å2
MethodPQS
4
M: FRUCTOSE-BISPHOSPHATE ALDOLASE B
N: FRUCTOSE-BISPHOSPHATE ALDOLASE B
O: FRUCTOSE-BISPHOSPHATE ALDOLASE B
P: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9398
Polymers157,5554
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint0.7 kcal/mol
Surface area60060 Å2
MethodPQS
5
Q: FRUCTOSE-BISPHOSPHATE ALDOLASE B
R: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules

Q: FRUCTOSE-BISPHOSPHATE ALDOLASE B
R: FRUCTOSE-BISPHOSPHATE ALDOLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9398
Polymers157,5554
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11080 Å2
ΔGint-37.6 kcal/mol
Surface area59990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)291.100, 489.840, 103.360
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.997097, 0.059797, -0.047146), (0.057579, 0.186908, -0.98068), (-0.049831, -0.98055, -0.189809)31.89326, 23.68275, 30.54217
2given(0.207074, 0.58658, 0.782962), (0.581788, -0.717254, 0.383487), (0.786538, 0.376107, -0.48979)-7.60802, -18.51731, 25.2832
3given(-0.216224, -0.640218, -0.737124), (-0.64009, -0.477142, 0.602172), (-0.737245, 0.602031, -0.306627)37.0628, -5.22755, 44.04025
4given(0.175317, 0.645276, 0.743549), (-0.84229, 0.489329, -0.226057), (-0.509717, -0.586651, 0.629297)33.99503, 134.25899, 31.97788
5given(-0.199484, -0.595778, -0.777971), (0.333719, 0.705164, -0.62559), (0.921325, -0.384419, 0.058153)4.14202, 148.2343, 69.562
6given(-0.852615, -0.027945, 0.521788), (0.516147, -0.20078, 0.832626), (0.081498, 0.979231, 0.185612)35.01218, 105.64614, 46.44726
7given(0.876264, -0.024725, -0.481192), (-0.020096, -0.999684, 0.014771), (-0.481412, -0.003274, -0.876483)22.53846, 129.8726, 88.42326
8given(0.137334, -0.627082, 0.766738), (-0.978069, -0.208227, 0.004884), (0.156596, -0.750595, -0.641927)154.68318, 172.33195, 100.24669
9given(-0.192802, 0.653234, -0.732185), (-0.342595, 0.654413, 0.674061), (0.919488, 0.380804, 0.097622)140.6729, 124.31854, 104.74457
10given(-0.414463, -0.84237, -0.344409), (0.84242, -0.498297, 0.205003), (-0.344312, -0.205169, 0.916156)175.63443, 161.88005, 78.30228
11given(0.48443, 0.817094, 0.312533), (0.470849, 0.057571, -0.880326), (-0.737312, 0.573612, -0.356839)171.71582, 116.91897, 100.16738
12given(-0.881863, -0.015392, 0.471249), (-0.461399, -0.177673, -0.869211), (0.097109, -0.983961, 0.149581)201.82765, 204.75586, 49.63222
13given(0.850343, 0.042395, -0.524513), (-0.230229, 0.926257, -0.298374), (0.473193, 0.374478, 0.797399)165.70456, 169.89792, 48.68849
14given(-0.376586, -0.880613, -0.287556), (-0.158175, -0.244726, 0.956594), (-0.912779, 0.405723, -0.047131)219.36765, 183.34608, 66.11924
15given(0.414615, 0.842096, 0.344896), (0.841324, -0.499163, 0.207378), (0.346798, 0.204186, -0.915439)175.575, 161.9614, 78.27222
16given(0.146885, 0.630515, 0.762135), (-0.666436, -0.506283, 0.547288), (0.730951, -0.588302, 0.345832)112.89944, 314.72992, 29.92561
17given(-0.204718, -0.626935, -0.751674), (-0.843052, 0.503132, -0.190039), (0.497348, 0.594796, -0.631539)123.99388, 304.53653, 77.53224
DetailsTHE BIOMOLECULE CONSISTS OF A HOMOTETRAMER AND 5 INDEPENDENTCOPIES ARE OBSERVED IN THE ASYMMETRIC UNIT WITH THE FIFTHTETRAMER REQUIRING CRYSTALLOGRAPHIC SYMMETRY.

-
Components

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE B / LIVER-TYPE ALDOLASE


Mass: 39388.773 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05062, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1169 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.65 Å3/Da / Density % sol: 79 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP WITH AMMONIUM SULFATE AS THE PRECIPITANT, pH 7.00

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.8
DetectorType: ADSC QUANTUM 4 CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 339612 / % possible obs: 71 % / Redundancy: 2.4 % / Biso Wilson estimate: 42.57 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.122 / Net I/σ(I): 3.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 0.4 / Rsym value: 0.438 / % possible all: 55.8

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ALD

2ald


Resolution: 2.5→29 Å / SU B: 9.96 / SU ML: 0.21655 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.40088 / ESU R Free: 0.30816 / Details: NCS RESTRAINTS USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.276 16667 5 %RANDOM
Rwork0.224 ---
obs-316146 71 %-
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48034 0 75 1169 49278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.01
X-RAY DIFFRACTIONp_angle_d0.0630.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0820.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it6.1474
X-RAY DIFFRACTIONp_mcangle_it7.6527
X-RAY DIFFRACTIONp_scbond_it12.2349
X-RAY DIFFRACTIONp_scangle_it13.149
X-RAY DIFFRACTIONp_plane_restr0.01880.02
X-RAY DIFFRACTIONp_chiral_restr0.2180.08
X-RAY DIFFRACTIONp_singtor_nbd0.2370.3
X-RAY DIFFRACTIONp_multtor_nbd0.3160.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2160.3
X-RAY DIFFRACTIONp_planar_tor5.86
X-RAY DIFFRACTIONp_staggered_tor22.310
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.420
X-RAY DIFFRACTIONp_special_tor010

+
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