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- PDB-1l6w: Fructose-6-phosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 1l6w
TitleFructose-6-phosphate aldolase
ComponentsFructose-6-phosphate aldolase 1
KeywordsLYASE / alpha-beta barrel / domain swapping
Function / homology
Function and homology information


ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel ...Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-6-phosphate aldolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.93 Å
AuthorsThorell, S. / Schuermann, M. / Sprenger, G.A. / Schneider, G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of decameric fructose-6-phosphate aldolase from Escherichia coli reveals inter-subunit helix swapping as a structural basis for assembly differences in the transaldolase family.
Authors: Thorell, S. / Schurmann, M. / Sprenger, G.A. / Schneider, G.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Fructose-6-phosphate Aldolase Is a Novel Class I Aldolase from Escherichia coli and Is Related to a Novel Group of Bacterial Transaldolases
Authors: Schuermann, M. / Sprenger, G.A.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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-6-phosphate aldolase 1
B: Fructose-6-phosphate aldolase 1
C: Fructose-6-phosphate aldolase 1
D: Fructose-6-phosphate aldolase 1
E: Fructose-6-phosphate aldolase 1
F: Fructose-6-phosphate aldolase 1
G: Fructose-6-phosphate aldolase 1
H: Fructose-6-phosphate aldolase 1
I: Fructose-6-phosphate aldolase 1
J: Fructose-6-phosphate aldolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,08920
Polymers230,16810
Non-polymers92110
Water26,6441479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41380 Å2
ΔGint-317 kcal/mol
Surface area69600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.490, 126.940, 183.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fructose-6-phosphate aldolase 1


Mass: 23016.756 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fsa / Plasmid: pUC18fsa / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1479 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMglycyl-glycine buffer1drop
31 mMdithiothreitol1droppH8.0
45.6-9 %(w/v)peg41reservoir
50.07 Msodium acetate1reservoirpH4.6
630 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.93→19.94 Å / Num. all: 200850 / Num. obs: 200177 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 11.3 Å2 / Limit h max: 59 / Limit h min: 0 / Limit k max: 65 / Limit k min: 0 / Limit l max: 95 / Limit l min: 0 / Observed criterion F max: 3950506.21 / Observed criterion F min: 11 / Rmerge(I) obs: 0.038 / Net I/σ(I): 46
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 18 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 200850 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 18

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIR / Resolution: 1.93→19.94 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 10079 5 %random
Rwork0.198 ---
obs-200173 99.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 60.0517 Å2 / ksol: 0.412232 e/Å3
Displacement parametersBiso max: 61.2 Å2 / Biso mean: 18.93 Å2 / Biso min: 6.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2---0.84 Å20 Å2
3----1.36 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Luzzati d res high-1.93
Refinement stepCycle: LAST / Resolution: 1.93→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16130 0 60 1479 17669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg22.6
X-RAY DIFFRACTIONx_torsion_impr_deg1.05
X-RAY DIFFRACTIONx_mcbond_it0.921.5
X-RAY DIFFRACTIONx_mcangle_it1.342
X-RAY DIFFRACTIONx_scbond_it2.012
X-RAY DIFFRACTIONx_scangle_it2.812.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.006 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.93-2.020.23112955.20.20223678250662497399.6
2.02-2.120.226125650.19623785250932504199.8
2.12-2.260.21412665.10.18923795250962506199.9
2.26-2.430.21512885.10.19623819251392510799.9
2.43-2.670.21913015.20.20223897252222519899.9
2.67-3.060.22412454.90.19923991252792523699.8
3.06-3.850.204124950.19623935253822518499.2
3.85-19.940.19811794.80.20223194259792437393.8
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.231 / Rfactor Rwork: 0.202 / Rfactor obs: 0.202

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