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- PDB-2quu: Dihydroxyacetone phosphate Schiff base intermediate in mutant fru... -

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Basic information

Entry
Database: PDB / ID: 2quu
TitleDihydroxyacetone phosphate Schiff base intermediate in mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / aldolase / mutant / substrate / Schiff base / protonated imine / intermediate / covalent / Acetylation / Glycolysis / 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
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSt-Jean, M. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Stereospecific proton transfer by a mobile catalyst in mammalian fructose-1,6-bisphosphate aldolase
Authors: St-Jean, M. / Sygusch, J.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600 HETEROGEN 13P LIGAND IS COVALENTLY BOUND TO LYS-229 AS A PROTONATED SCHIFF BASE (IMINIUM) INTERMEDIATE.

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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)157,7438
Polymers157,0634
Non-polymers6804
Water40,1732230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.858, 103.722, 84.881
Angle α, β, γ (deg.)90.000, 98.771, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the homotetramer found in the asymmetric unit

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Components

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


Mass: 39265.688 Da / Num. of mol.: 4 / Mutation: K146M
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 / Dihydroxyacetone phosphate


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


Mass: 18.015 Da / Num. of mol.: 2230 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsREMARK 600 HETEROGEN REMARK 600 13P LIGAND IS COVALENTLY BOUND TO LYS-229 AS A SCHIFF BASE ...REMARK 600 HETEROGEN REMARK 600 13P LIGAND IS COVALENTLY BOUND TO LYS-229 AS A SCHIFF BASE INTERMEDIATE (PROTONATED IMINE).

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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: 47.05 %
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 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 109942 / % possible obs: 88.1 % / Redundancy: 3.4 % / Rsym value: 0.052 / Χ2: 1.091 / Net I/σ(I): 21.4
Reflection shellResolution: 1.84→1.91 Å / Num. unique all: 5901 / Χ2: 1.011 / % possible all: 47.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZAH

1zah


Resolution: 1.98→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.195 8893 -random
Rwork0.157 ---
all-96349 --
obs-89297 89.4 %-
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.402 Å20 Å21.958 Å2
2---5.78 Å20 Å2
3---5.379 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10820 0 36 2230 13086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.211
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.98→2.07 Å
RfactorNum. reflection% reflection
Rfree0.248 732 -
Rwork0.213 --
obs-7353 59.2 %

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