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- PDB-6xml: Human aldolase A I98C -

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Basic information

Entry
Database: PDB / ID: 6xml
TitleHuman aldolase A I98C
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: 1.88 Å
AuthorsMeneely, K.M. / Brewer, K. / 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)79,85212
Polymers78,9202
Non-polymers93210
Water4,522251
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)159,70524
Polymers157,8404
Non-polymers1,86520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area13150 Å2
ΔGint-91 kcal/mol
Surface area50290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.571, 162.571, 167.797
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-404-

GOL

21A-618-

HOH

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Components

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


Mass: 39459.965 Da / Num. of mol.: 2 / Mutation: I98C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOA, ALDA / Plasmid: pET15b / 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.: 251 / 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: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% (w/v) PEG 8000, 21% (v/v) glycerol in 0.04 M potassium phosphate, pH 6.0

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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: 1.88→107.85 Å / Num. obs: 65292 / % possible obs: 94.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 37.08 Å2 / Rpim(I) all: 0.027 / Net I/σ(I): 14.4
Reflection shellResolution: 1.88→2.08 Å / Num. unique obs: 3266 / Rpim(I) all: 0.347

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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: 1.88→40.2 Å / SU ML: 0.3003 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.4471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2856 3139 4.81 %
Rwork0.2451 62114 -
obs0.247 65253 61.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.11 Å2
Refinement stepCycle: LAST / Resolution: 1.88→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 56 251 5693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02355530
X-RAY DIFFRACTIONf_angle_d1.86177482
X-RAY DIFFRACTIONf_chiral_restr0.0753846
X-RAY DIFFRACTIONf_plane_restr0.0114967
X-RAY DIFFRACTIONf_dihedral_angle_d24.69482049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.910.45880.3658204X-RAY DIFFRACTION4.49
1.91-1.940.5034170.3802365X-RAY DIFFRACTION8.2
1.94-1.970.3968260.3482519X-RAY DIFFRACTION11.51
1.97-2.010.3966400.3566664X-RAY DIFFRACTION14.85
2.01-2.050.3297310.3893822X-RAY DIFFRACTION18.03
2.05-2.090.4639380.3655725X-RAY DIFFRACTION16.09
2.09-2.140.3938570.33841151X-RAY DIFFRACTION25.51
2.14-2.190.3142530.33511348X-RAY DIFFRACTION29.47
2.19-2.240.382790.33081639X-RAY DIFFRACTION36.12
2.24-2.30.3919990.3421888X-RAY DIFFRACTION41.82
2.3-2.370.42041440.3552907X-RAY DIFFRACTION64.12
2.37-2.450.37161930.34883987X-RAY DIFFRACTION87.39
2.45-2.530.37632280.35034522X-RAY DIFFRACTION99.27
2.53-2.630.3292360.33164536X-RAY DIFFRACTION99.87
2.63-2.750.33262120.32374198X-RAY DIFFRACTION91.55
2.75-2.90.3532370.31614559X-RAY DIFFRACTION99.83
2.9-3.080.35232350.29034577X-RAY DIFFRACTION99.94
3.08-3.320.30082460.26554595X-RAY DIFFRACTION99.9
3.32-3.650.3052120.23124651X-RAY DIFFRACTION99.98
3.65-4.180.22992310.18724644X-RAY DIFFRACTION99.94
4.18-5.270.22312470.16844695X-RAY DIFFRACTION99.84
5.27-40.20.22622700.19734918X-RAY DIFFRACTION99.48

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