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- PDB-3dfo: Dihydroxyacetone phosphate Schiff base and enamine intermediates ... -

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Basic information

Entry
Database: PDB / ID: 3dfo
TitleDihydroxyacetone phosphate Schiff base and enamine intermediates in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / aldolase / mutant / iminium / Schiff base / enamine / intermediate / covalent
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: 1.94 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 1.4Nov 6, 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

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)157,7318
Polymers157,0514
Non-polymers6804
Water37,4532079
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-41.1 kcal/mol
Surface area48800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.676, 103.132, 84.562
Angle α, β, γ (deg.)90.00, 98.71, 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: 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.: 2079 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details13P LIGAND IS COVALENTLY BOUND TO LYS-229 AS AN IMINIUM OR AN ENAMINE 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 296 K / pH: 7.5
Details: sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 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: 118077 / % possible obs: 90 % / Redundancy: 3.3 % / Rsym value: 0.083 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1 / Rsym value: 0.699 / % possible all: 50.1

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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: 1.94→43.76 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.199 9029 -RANDOM
Rwork0.152 ---
obs0.152 89723 85.5 %-
all-102541 --
Displacement parametersBiso mean: 25.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.492 Å20 Å21.914 Å2
2---5.703 Å20 Å2
3---6.196 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.94→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10780 0 36 2079 12895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.24
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.59
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
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: 1.94→2.03 Å
RfactorNum. reflection% reflection
Rfree0.2815 684 -
Rwork0.2489 --
obs--52.8 %

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