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- PDB-1xdm: Structure of human aldolase B associated with hereditary fructose... -

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Basic information

Entry
Database: PDB / ID: 1xdm
TitleStructure of human aldolase B associated with hereditary fructose intolerance (A149P), at 291K
ComponentsFructose-bisphosphate aldolase B
KeywordsLYASE / ALPHA/BETA BARREL
Function / homology
Function and homology information


fructose-1-phosphate aldolase activity / Hereditary fructose intolerance / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / NADH oxidation / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process ...fructose-1-phosphate aldolase activity / Hereditary fructose intolerance / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / NADH oxidation / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / Gluconeogenesis / positive regulation of ATP-dependent activity / negative regulation of pentose-phosphate shunt / Glycolysis / microtubule organizing center / centriolar satellite / cytoskeletal protein binding / gluconeogenesis / glycolytic process / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMalay, A.D. / Allen, K.N. / Tolan, D.R.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance.
Authors: Malay, A.D. / Allen, K.N. / Tolan, D.R.
#1: Journal: Arch.Biochem.Biophys. / Year: 2002
Title: The temperature dependence of activity and structure for the most prevalent mutant aldolase B associated with hereditary fructose intolerance
Authors: Malay, A.D. / Procious, S.L. / Tolan, D.R.
History
DepositionSep 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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 B
B: Fructose-bisphosphate aldolase B
C: Fructose-bisphosphate aldolase B
D: Fructose-bisphosphate aldolase B
W: Fructose-bisphosphate aldolase B
X: Fructose-bisphosphate aldolase B
Y: Fructose-bisphosphate aldolase B
Z: Fructose-bisphosphate aldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,24016
Polymers316,4728
Non-polymers7698
Water63135
1
A: Fructose-bisphosphate aldolase B
B: Fructose-bisphosphate aldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3104
Polymers79,1182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-33 kcal/mol
Surface area24560 Å2
MethodPISA
2
C: Fructose-bisphosphate aldolase B
D: Fructose-bisphosphate aldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3104
Polymers79,1182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-29 kcal/mol
Surface area24080 Å2
MethodPISA
3
W: Fructose-bisphosphate aldolase B
X: Fructose-bisphosphate aldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3104
Polymers79,1182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-29 kcal/mol
Surface area24380 Å2
MethodPISA
4
Y: Fructose-bisphosphate aldolase B
Z: Fructose-bisphosphate aldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3104
Polymers79,1182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-33 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.421, 153.475, 185.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit of AP-aldolase is a dimer, corresponding to monomer pairs AB, CD, WX, and YZ. The wild-type enzyme is tetrameric.

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Components

#1: Protein
Fructose-bisphosphate aldolase B / Liver-type aldolase


Mass: 39558.938 Da / Num. of mol.: 8 / Mutation: A149P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOB, ALDB / Plasmid: pGEX-AP / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P05062, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, 1,8-diaminooctane, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 13, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 87953 / Num. obs: 83595 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.067 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 7680 / Rsym value: 0.364 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QO5

1qo5


Resolution: 3→79.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 295432.84 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: used ncs restraints between monomers
RfactorNum. reflection% reflectionSelection details
Rfree0.319 7920 10 %RANDOM
Rwork0.271 ---
all0.288 83595 --
obs0.276 79141 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.4177 Å2 / ksol: 0.294477 e/Å3
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1-16.2 Å20 Å20 Å2
2--12.39 Å20 Å2
3----28.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a1.15 Å1.02 Å
Refinement stepCycle: LAST / Resolution: 3→79.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18475 0 40 35 18550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.448 650 10.8 %
Rwork0.437 5370 -
obs-7735 69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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