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- PDB-3b8d: Fructose 1,6-bisphosphate aldolase from rabbit muscle -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3b8d
TitleFructose 1,6-bisphosphate aldolase from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / ALDOLASE / LYASE(ALDEHYDE) / SCHIFF BASE / GLYCOLYSIS / Acetylation / Phosphorylation
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / glycolytic process / protein homotetramerization / positive regulation of cell migration
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 A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaurady, A. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: A conserved glutamate residue exhibits multifunctional catalytic roles in D-fructose-1,6-bisphosphate aldolases.
Authors: Maurady, A. / Zdanov, A. / De Moissac, D. / Beaudry, D. / Sygusch, J.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 13, 2007ID: 1EWG
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,2436
Polymers157,0514
Non-polymers1922
Water62,1883452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.32, 57.51, 85.36
Angle α, β, γ (deg.)90.00, 102.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fructose-bisphosphate aldolase A / Muscle-type aldolase


Mass: 39262.688 Da / Num. of mol.: 4 / Mutation: E188Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: PPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHAMCR / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3452 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 7.4
Details: 40% ammonium sulphate 5mM EDTA, 100mM triethylamine, pH 7.4, SMALL TUBES, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 88143 / Num. obs: 87623

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: XPLOR parhcsdx
RfactorNum. reflectionSelection details
Rfree0.238 6958 RANDOM
Rwork0.189 --
all-87623 -
obs-87623 -
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11032 0 10 3452 14494
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.568
X-RAY DIFFRACTIONx_angle_diedre21.474
X-RAY DIFFRACTIONx_torsion_impr_deg1.27

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