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- PDB-3dfs: Dihydroxyacetone phosphate Schiff base intermediate in D33S mutan... -

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Basic information

Entry
Database: PDB / ID: 3dfs
TitleDihydroxyacetone phosphate Schiff base intermediate in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / aldolase / mutant / iminium / Schiff base / intermediate / covalent / Acetylation / Glycolysis / Phosphoprotein
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
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Fructose-bisphosphate aldolase A
D: Fructose-bisphosphate aldolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6238
Polymers156,9434
Non-polymers6804
Water38,1922120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-42 kcal/mol
Surface area48920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.883, 103.797, 84.814
Angle α, β, γ (deg.)90.00, 98.91, 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: 39235.660 Da / Num. of mol.: 4 / Mutation: D33S
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: Chemical
ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details13P LIGAND IS COVALENTLY BOUND TO LYS-229 AS AN IMINIUM INTERMEDIATE.

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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: 2.32 Å3/Da / Density % sol: 47.08 %
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: Mar 15, 2006
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: 109998 / % possible obs: 82.4 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4669 / Rsym value: 0.528 / % possible all: 35.1

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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: 2.03→44.11 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.187 8607 -random
Rwork0.141 ---
all-90225 --
obs-85170 91.9 %-
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.122 Å20 Å20.735 Å2
2---3.487 Å20 Å2
3---3.609 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.03→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10759 0 36 2120 12915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.216
X-RAY DIFFRACTIONc_dihedral_angle_d21.572
X-RAY DIFFRACTIONc_improper_angle_d0.896
LS refinement shellResolution: 2.03→2.13 Å
RfactorNum. reflection% reflection
Rfree0.211 1032 -
Rwork0.166 --
obs-10197 77.1 %

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