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- PDB-4rxg: Fructose-6-phosphate aldolase Q59E from E.coli -

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Basic information

Entry
Database: PDB / ID: 4rxg
TitleFructose-6-phosphate aldolase Q59E from E.coli
ComponentsFructose-6-phosphate aldolase 1
KeywordsLYASE / Tim barrel / homodecamer / FSA / TalB
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 / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsStellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
CitationJournal: ChemCatChem / Year: 2015
Title: Acid Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase
Authors: Stellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)232,25831
Polymers230,17710
Non-polymers2,08021
Water15,223845
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45090 Å2
ΔGint-313 kcal/mol
Surface area69290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.436, 126.748, 183.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.305207, 0.043476, 0.951293), (-0.059815, 0.99786, -0.026413), (-0.950406, -0.04884, 0.307155)60.64001, -0.66714, -23.45236
3given(-0.809408, 0.002969, 0.587239), (-0.074516, 0.991385, -0.10772), (-0.5825, -0.130948, -0.802214)56.93771, -4.47256, -88.10684
4given(-0.805746, -0.092148, -0.585049), (-0.022593, 0.991885, -0.125111), (0.59183, -0.08759, -0.80129)-5.79782, -6.56538, -104.51708
5given(0.314938, -0.052946, -0.947634), (0.025781, 0.998552, -0.047223), (0.948762, -0.009559, 0.315847)-40.97388, -2.45339, -49.80267
6given(0.606042, -0.028695, -0.794915), (-0.020801, -0.999579, 0.020224), (-0.795161, 0.004278, -0.606384)-36.8465, -9.78452, -73.84
7given(0.942891, 0.059236, 0.327791), (0.056027, -0.998244, 0.019235), (0.328355, 0.000229, -0.944554)18.55011, -11.19024, -107.81445
8given(-0.028223, 0.096744, 0.994909), (0.079803, -0.991911, 0.098716), (0.996411, 0.082183, 0.020274)68.04797, -7.63297, -65.70105
9given(-0.958641, 0.007667, 0.284514), (0.029591, -0.991535, 0.126422), (0.283074, 0.129612, 0.9503)43.03128, -5.05995, -5.94351
10given(-0.569318, -0.045589, -0.820852), (-0.025644, -0.996991, 0.073158), (-0.821717, 0.0627, 0.566436)-21.43727, -7.29823, -10.83457

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Components

#1: Protein
Fructose-6-phosphate aldolase 1 / Fructose-6-phosphate aldolase A / FSAA


Mass: 23017.740 Da / Num. of mol.: 10 / Mutation: Q59E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0825, fsa, fsaA, JW5109, mipB, ybiZ / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha
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.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / 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: 57.81 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 1, 2004
RadiationMonochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.154→104.5 Å / Num. all: 145571 / Num. obs: 142189 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.154→2.57 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6W

1l6w


Resolution: 2.154→104.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.009 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22807 7137 5 %RANDOM
Rwork0.18868 ---
all0.19066 135052 --
obs0.19066 135052 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å20 Å2
2---0.09 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.154→104.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16130 0 130 845 17105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916489
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216562
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.99122388
X-RAY DIFFRACTIONr_angle_other_deg0.812338087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8652190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64825.273550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.061152740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.251560
X-RAY DIFFRACTIONr_chiral_restr0.0810.22750
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023250
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.382.3338790
X-RAY DIFFRACTIONr_mcbond_other1.382.3338789
X-RAY DIFFRACTIONr_mcangle_it2.1513.49310970
X-RAY DIFFRACTIONr_mcangle_other2.1513.49310971
X-RAY DIFFRACTIONr_scbond_it2.1472.5977699
X-RAY DIFFRACTIONr_scbond_other2.1472.5977700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3763.7611419
X-RAY DIFFRACTIONr_long_range_B_refined4.54918.90618826
X-RAY DIFFRACTIONr_long_range_B_other4.54918.90718827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 345 -
Rwork0.313 7569 -
obs--74.06 %

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