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- PDB-1xfb: Human Brain Fructose 1,6-(bis)phosphate Aldolase (C isozyme) -

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Basic information

Entry
Database: PDB / ID: 1xfb
TitleHuman Brain Fructose 1,6-(bis)phosphate Aldolase (C isozyme)
ComponentsAldolase C
KeywordsLYASE / isozyme specificity / structural enzymology / protein-protein interactions / isozyme specific residues / structure/function
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / Glycolysis / cytoskeletal protein binding / epithelial cell differentiation / glycolytic process / gluconeogenesis ...fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / Glycolysis / cytoskeletal protein binding / epithelial cell differentiation / glycolytic process / gluconeogenesis / tertiary granule lumen / secretory granule lumen / ficolin-1-rich granule lumen / cytoskeleton / Neutrophil degranulation / extracellular exosome / extracellular region / 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 C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArakaki, T.L. / Pezza, J.A. / Cronin, M.A. / Hopkins, C.E. / Zimmer, D.B. / Tolan, D.R. / Allen, K.N.
CitationJournal: Protein Sci. / Year: 2004
Title: Structure of human brain fructose 1,6-(bis)phosphate aldolase: linking isozyme structure with function
Authors: Arakaki, T.L. / Pezza, J.A. / Cronin, M.A. / Hopkins, C.E. / Zimmer, D.B. / Tolan, D.R. / Allen, K.N.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldolase C
B: Aldolase C
C: Aldolase C
D: Aldolase C
E: Aldolase C
F: Aldolase C
G: Aldolase C
H: Aldolase C
I: Aldolase C
J: Aldolase C
K: Aldolase C
L: Aldolase C


Theoretical massNumber of molelcules
Total (without water)475,40412
Polymers475,40412
Non-polymers00
Water00
1
A: Aldolase C
B: Aldolase C
C: Aldolase C
D: Aldolase C


Theoretical massNumber of molelcules
Total (without water)158,4684
Polymers158,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Aldolase C
F: Aldolase C
G: Aldolase C
H: Aldolase C


Theoretical massNumber of molelcules
Total (without water)158,4684
Polymers158,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Aldolase C
J: Aldolase C
K: Aldolase C
L: Aldolase C


Theoretical massNumber of molelcules
Total (without water)158,4684
Polymers158,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.872, 121.986, 129.517
Angle α, β, γ (deg.)107.96, 108.58, 97.39
Int Tables number1
Space group name H-MP1
DetailsTetramer of molecules A, B, C, D / Tetramer of molecules E, F, G, H / Tetramer of molecules I, J, K, L

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Components

#1: Protein
Aldolase C / Fructose 1 / 6-(bis)phosphate Aldolase


Mass: 39616.973 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P09972, fructose-bisphosphate aldolase

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Calcium Acetate, Tris, glucose, pH 8.0, 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: Feb 1, 2003 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→79.24 Å / Num. all: 89550 / Num. obs: 89550 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 27 / Limit h min: -29 / Limit k max: 41 / Limit k min: -29 / Limit l max: 46 / Limit l min: 0 / Observed criterion F max: 1989158.51 / Observed criterion F min: 6.4 / Rsym value: 0.097 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.15 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.34 / % possible all: 95.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1J4E

1j4e


Resolution: 3→79.24 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 8700 10 %random
Rwork0.255 ---
all0.257 89706 --
obs0.257 87177 97.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 30.8274 Å2 / ksol: 0.370575 e/Å3
Displacement parametersBiso max: 99.51 Å2 / Biso mean: 35.37 Å2 / Biso min: 0.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å27.22 Å22.25 Å2
2--9.79 Å28.67 Å2
3----6.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.67 Å
Luzzati d res high-3
Refinement stepCycle: LAST / Resolution: 3→79.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31476 0 0 0 31476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg21.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3-3.140.382111810.40.38596020.011112201072095.5
3.14-3.30.3310289.50.33997540.01112191078296.1
3.3-3.510.313111310.20.397610.009112731087496.5
3.51-3.780.28110549.70.27398000.009111801085497.1
3.78-4.160.25110410.10.2498250.008112081092997.5
4.16-4.760.22210749.70.20799540.007112591102897.9
4.76-60.2181098100.21799150.007112081101398.3
6-79.240.212111110.10.20998660.006112071097797.9
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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