[English] 日本語
Yorodumi
- PDB-6xmh: Human aldolase A wild type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xmh
TitleHuman aldolase A wild type
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / rheostat / allosterism
Function / homology
Function and homology information


fructose binding / sperm head / fructose-bisphosphate aldolase / ATP biosynthetic process / fructose-bisphosphate aldolase activity / binding of sperm to zona pellucida / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / M band ...fructose binding / sperm head / fructose-bisphosphate aldolase / ATP biosynthetic process / fructose-bisphosphate aldolase activity / binding of sperm to zona pellucida / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / M band / Glycolysis / I band / muscle cell cellular homeostasis / striated muscle contraction / cytoskeletal protein binding / tubulin binding / platelet alpha granule lumen / actin filament organization / glycolytic process / tertiary granule lumen / Platelet degranulation / regulation of cell shape / actin cytoskeleton / actin binding / secretory granule lumen / protein homotetramerization / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / 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-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMeneely, K.M. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)77619 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Substitutions at a rheostat position in human aldolase A cause a shift in the conformational population.
Authors: Fenton, K.D. / Meneely, K.M. / Wu, T. / Martin, T.A. / Swint-Kruse, L. / Fenton, A.W. / Lamb, A.L.
History
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-bisphosphate aldolase A
B: Fructose-bisphosphate aldolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,96513
Polymers78,9402
Non-polymers1,02511
Water4,089227
1
A: Fructose-bisphosphate aldolase A
B: Fructose-bisphosphate aldolase A
hetero molecules

A: Fructose-bisphosphate aldolase A
B: Fructose-bisphosphate aldolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,92926
Polymers157,8804
Non-polymers2,04922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Unit cell
Length a, b, c (Å)161.885, 161.885, 168.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21A-608-

HOH

-
Components

#1: Protein Fructose-bisphosphate aldolase A / Lung cancer antigen NY-LU-1 / Muscle-type aldolase


Mass: 39469.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOA, ALDA / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P04075, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.75
Details: 10% (w/v) PEG 8,000, 18% (v/v) glycerol, 0.04 M potassium phosphate, pH 5.75

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2019
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→140.2 Å / Num. obs: 549062 / % possible obs: 93.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 34.86 Å2 / Rpim(I) all: 0.046 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→2.2 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2830 / Rpim(I) all: 0.356

-
Processing

Software
NameVersionClassification
REFMAC1.16_3549refinement
PHENIX1.16_3549refinement
autoPROCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ALD

1ald


Resolution: 1.95→40.85 Å / SU ML: 0.2805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.4293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2861 2803 4.95 %
Rwork0.2386 53769 -
obs0.241 56572 60.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.93 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 62 227 5668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01595529
X-RAY DIFFRACTIONf_angle_d1.54287479
X-RAY DIFFRACTIONf_chiral_restr0.0643846
X-RAY DIFFRACTIONf_plane_restr0.0088963
X-RAY DIFFRACTIONf_dihedral_angle_d24.85852049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.343930.23688X-RAY DIFFRACTION1.99
1.99-2.020.3238140.3581258X-RAY DIFFRACTION5.93
2.02-2.060.4164190.349417X-RAY DIFFRACTION9.41
2.06-2.10.3349250.3795394X-RAY DIFFRACTION9.09
2.1-2.150.368340.3333689X-RAY DIFFRACTION15.71
2.15-2.20.366470.3557905X-RAY DIFFRACTION20.57
2.2-2.250.3274430.3668954X-RAY DIFFRACTION21.5
2.25-2.320.3475790.34771353X-RAY DIFFRACTION30.94
2.32-2.380.3763790.33871844X-RAY DIFFRACTION41.27
2.38-2.460.37331570.34212790X-RAY DIFFRACTION63.44
2.46-2.550.38982140.34313907X-RAY DIFFRACTION88.57
2.55-2.650.35072500.33464388X-RAY DIFFRACTION99.02
2.65-2.770.36831790.33234078X-RAY DIFFRACTION91.08
2.77-2.920.36822350.30424456X-RAY DIFFRACTION99.91
2.92-3.10.31272480.28254439X-RAY DIFFRACTION99.98
3.1-3.340.32562310.25074504X-RAY DIFFRACTION100
3.34-3.680.29392020.2234397X-RAY DIFFRACTION96.92
3.68-4.210.24232650.18354490X-RAY DIFFRACTION99.94
4.21-5.30.20882230.16484618X-RAY DIFFRACTION99.9
5.3-40.850.22892560.19444800X-RAY DIFFRACTION99.43

+
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