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- PDB-6xmh: Human aldolase A wild type -

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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 / 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: 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

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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)79,96513
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

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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

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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: 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

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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

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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

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