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- PDB-6xmo: Human aldolase A I98F -

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Basic information

Entry
Database: PDB / ID: 6xmo
TitleHuman aldolase A I98F
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 / actin cytoskeleton / regulation of cell shape / 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: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,94012
Polymers79,0082
Non-polymers93210
Water59433
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)159,88124
Polymers158,0164
Non-polymers1,86520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area13020 Å2
ΔGint-84 kcal/mol
Surface area46480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.682, 159.682, 165.306
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-515-

HOH

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Components

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


Mass: 39503.996 Da / Num. of mol.: 2 / Mutation: I98F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOA, ALDA / 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.75
Details: 12% (w/v) PEG 8000, 15% (v/v) glycerol, 0.04 M potassium phosphate, pH 5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2019
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→138.29 Å / Num. obs: 26180 / % possible obs: 89.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 47.71 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.84 Å / Num. unique obs: 1309 / Rpim(I) all: 0.425

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Processing

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

1ald


Resolution: 2.6→53.03 Å / SU ML: 0.256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 1271 4.86 %
Rwork0.2129 24870 -
obs0.2153 26141 67.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.71 Å2
Refinement stepCycle: LAST / Resolution: 2.6→53.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 56 33 5471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01695528
X-RAY DIFFRACTIONf_angle_d1.75787478
X-RAY DIFFRACTIONf_chiral_restr0.0663844
X-RAY DIFFRACTIONf_plane_restr0.012964
X-RAY DIFFRACTIONf_dihedral_angle_d25.83072042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.7000.210311X-RAY DIFFRACTION0.26
2.7-2.830.3553470.33321115X-RAY DIFFRACTION27.59
2.83-2.970.3436700.31251687X-RAY DIFFRACTION41.45
2.97-3.160.40341110.30672530X-RAY DIFFRACTION62.29
3.16-3.40.31942120.26773840X-RAY DIFFRACTION94.56
3.4-3.750.29351700.23263080X-RAY DIFFRACTION75.6
3.75-4.290.22352190.17774088X-RAY DIFFRACTION99.91
4.29-5.40.23222130.1734162X-RAY DIFFRACTION99.93
5.4-53.030.22362290.20084357X-RAY DIFFRACTION99.24

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