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- PDB-4rxf: Fructose-6-phosphate aldolase Y131F from E.coli -

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Basic information

Entry
Database: PDB / ID: 4rxf
TitleFructose-6-phosphate aldolase Y131F from E.coli
ComponentsFructose-6-phosphate aldolase 1
KeywordsLYASE / Tim barrel / homodecamer / FSAA 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
PHOSPHATE ION / Fructose-6-phosphate aldolase 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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_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_ref_seq_dif.details / _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)239,24620
Polymers238,29610
Non-polymers95010
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41460 Å2
ΔGint-358 kcal/mol
Surface area71340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.400, 133.602, 101.590
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.724079, 0.209273, 0.657202), (0.45251, 0.574972, -0.681646), (-0.520523, 0.790956, 0.321628)-10.74007, 7.168, 28.75562
3given(0.285497, 0.794544, 0.535902), (0.938437, -0.118288, -0.324567), (-0.194492, 0.595573, -0.779401)1.96636, -12.60534, 49.57709
4given(0.279309, 0.940456, -0.193724), (0.80061, -0.116714, 0.587709), (0.530104, -0.31925, -0.785538)20.67961, -32.92289, 33.82541
5given(0.727013, 0.451745, -0.517087), (0.216431, 0.563924, 0.796962), (0.651621, -0.691315, 0.312208)19.19628, -25.29904, 3.08677
6given(-0.744339, -0.426941, 0.513499), (-0.429552, -0.282657, -0.857665), (0.511316, -0.858968, 0.026999)25.34894, 31.0865, 13.43532
7given(-0.99965, 0.011446, -0.023852), (-0.002074, -0.932693, -0.360664), (-0.026375, -0.360489, 0.932391)44.54718, 9.05639, 2.34052
8given(-0.71509, -0.214328, -0.665365), (-0.244783, -0.814794, 0.525539), (-0.654773, 0.538678, 0.530187)54.50525, -8.42051, 26.37306
9given(-0.277826, -0.810147, -0.516211), (-0.806942, -0.09474, 0.582983), (-0.521209, 0.57852, -0.62742)41.36794, 2.81579, 52.86593
10given(-0.284471, -0.93782, 0.198921), (-0.930883, 0.220603, -0.291189), (0.2292, -0.268007, -0.935756)22.87686, 27.32549, 44.32247

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Components

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


Mass: 23829.637 Da / Num. of mol.: 10 / Mutation: Y131F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b0825, fsa, fsaA, JW5109, mipB, ybiZ / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS*
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% PEG3350, 0.1M HEPES pH 8, 0.2M LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91844 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91844 Å / Relative weight: 1
ReflectionResolution: 2.4→101.49 Å / Num. all: 91562 / Num. obs: 91562 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6W

1l6w


Resolution: 2.4→101.49 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.099 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 4612 5 %RANDOM
Rwork0.19392 ---
obs0.19595 86941 99.48 %-
all-86941 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-0 Å20.44 Å2
2---1.54 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.4→101.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16140 0 50 214 16404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216490
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.98422380
X-RAY DIFFRACTIONr_angle_other_deg0.761337890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47652190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43925.179560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.033152720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6051560
X-RAY DIFFRACTIONr_chiral_restr0.0650.22730
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023320
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_it1.1382.6128790
X-RAY DIFFRACTIONr_mcbond_other1.1372.6118789
X-RAY DIFFRACTIONr_mcangle_it1.8673.91210970
X-RAY DIFFRACTIONr_mcangle_other1.8863.95210971
X-RAY DIFFRACTIONr_scbond_it1.4432.817650
X-RAY DIFFRACTIONr_scbond_other1.4592.8447641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4384.16211375
X-RAY DIFFRACTIONr_long_range_B_refined3.76720.70217682
X-RAY DIFFRACTIONr_long_range_B_other3.76720.70317683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 338 -
Rwork0.23 6365 -
obs--99.05 %

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