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- PDB-3dfn: D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle -

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Basic information

Entry
Database: PDB / ID: 3dfn
TitleD33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / aldolase / mutant / Acetylation / Glycolysis / Phosphoprotein / Schiff base
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSt-Jean, M. / Sygusch, J.
CitationJournal: Biochemistry / Year: 2009
Title: Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase
Authors: St-Jean, M. / Blonski, C. / Sygusch, J.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 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

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


Theoretical massNumber of molelcules
Total (without water)157,0514
Polymers157,0514
Non-polymers00
Water40,8042265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11110 Å2
ΔGint-37.2 kcal/mol
Surface area49590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.247, 103.868, 84.882
Angle α, β, γ (deg.)90.00, 98.87, 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: D33N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: pPB14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 SI / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2265 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 121528 / % possible obs: 91 % / Redundancy: 3 % / Rsym value: 0.069 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 7936 / Rsym value: 0.274 / % possible all: 59.6

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZAH

1zah


Resolution: 1.86→44.07 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.188 9973 -random
Rwork0.141 ---
all-114108 --
obs-99123 81.9 %-
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.823 Å20 Å20.728 Å2
2---3.243 Å20 Å2
3---4.066 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10813 0 0 2265 13078
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.201
X-RAY DIFFRACTIONc_dihedral_angle_d21.598
X-RAY DIFFRACTIONc_improper_angle_d0.871
LS refinement shellResolution: 1.86→1.94 Å
RfactorNum. reflection% reflection
Rfree0.199 678 -
Rwork0.171 --
obs-6656 44.9 %

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