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- PDB-1e47: L-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant E73Q -

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Basic information

Entry
Database: PDB / ID: 1.0E+47
TitleL-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant E73Q
ComponentsL-FUCULOSE 1-PHOSPHATE ALDOLASE
KeywordsALDOLASE (CLASS II) / BACTERIAL L-FUCOSE METABOLISM / CLEAVAGE OF L-FUCULOSE 1-PHOSPHATE TO DIHYDROXYACETONE PHOSPHATE AND L-LACTALDEHYDE / MUTANT STRUCTURE
Function / homology
Function and homology information


D-arabinose catabolic process / L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / L-fucose catabolic process / pentose catabolic process / aldehyde-lyase activity / zinc ion binding / cytosol
Similarity search - Function
L-fucose phosphate aldolase / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / BETA-MERCAPTOETHANOL / L-fuculose phosphate aldolase / L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.15 Å
AuthorsJoerger, A.C. / Schulz, G.E.
Citation
Journal: J. Mol. Biol. / Year: 2000
Title: Structures of l-fuculose-1-phosphate aldolase mutants outlining motions during catalysis.
Authors: Joerger, A.C. / Mueller-Dieckmann, C. / Schulz, G.E.
#1: Journal: Biochemistry / Year: 2000
Title: Catalytic Action of Fuculose 1-Phosphate Aldolase (Class II) as Derived by Structure-Directed Mutagenesis
Authors: Joerger, A.C. / Gosse, C. / Fessner, W.-D. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Catalytic Mechanism of the Metal-Dependent Fuculose Aldolase from Escherichia Coli as Derived from the Structure
Authors: Dreyer, M.K. / Schulz, G.E.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: The Spatial Structure of the Class II L-Fuculose-1-Phosphate Aldolase from Escherichia Coli
Authors: Dreyer, M.K. / Schulz, G.E.
History
DepositionJun 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: L-FUCULOSE 1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3106
Polymers23,8041
Non-polymers5065
Water2,108117
1
P: L-FUCULOSE 1-PHOSPHATE ALDOLASE
hetero molecules

P: L-FUCULOSE 1-PHOSPHATE ALDOLASE
hetero molecules

P: L-FUCULOSE 1-PHOSPHATE ALDOLASE
hetero molecules

P: L-FUCULOSE 1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,24024
Polymers95,2174
Non-polymers2,02320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.900, 93.900, 43.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsBIOMOLECULE

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Components

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Protein , 1 types, 1 molecules P

#1: Protein L-FUCULOSE 1-PHOSPHATE ALDOLASE


Mass: 23804.334 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: E73Q MUTATION PERFORMED WITH PHOSPHOROTHIOATE METHOD USING M13MP19
Plasmid: PKKFA2-E73Q / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 105
References: UniProt: P11550, UniProt: P0AB87*PLUS, L-fuculose-phosphate aldolase

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN P ENGINEERED MUTATION GLU73GLN

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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 Å3/Da / Density % sol: 39 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS GROWN FROM AMMONIUM SULFATE AT PH 8.0, VAPOUR DIFFUSION, HANGING DROP, CONDITIONS CLOSE TO THE ONES REPORTED FOR THE WILD-TYPE, SEE PDB ID 1FUA FOR FURTHER DETAILS
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.6 / Method: vapor diffusion, hanging drop
Details: Dreyer, M.K., (1996) Acta Crystallog. sect., D52, 1082.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
30.5 mM1dropZnCl2
410 mMbeta-mercaptoethanol1drop
51.62 Mammonium sulfate1reservoir
620 mMpotassium phosphate1reservoir
74 mM1reservoirZnCl2
84 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MULTIWIRE SIEMENS X-100 / Detector: AREA DETECTOR / Date: Jul 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→10 Å / Num. obs: 10320 / % possible obs: 95 % / Redundancy: 3.4 % / Rsym value: 0.044 / Net I/σ(I): 16
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 6 / Rsym value: 0.13 / % possible all: 87
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 87 % / Num. unique obs: 861 / Rmerge(I) obs: 0.13

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 2.15→10 Å / SU B: 2.8 / SU ML: 0.07 / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.19
Details: THE 9 C-TERMINAL RESIDUES (LYS207 - GLU 215) WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 -6 %RANDOM
Rwork0.15 ---
obs-10320 95 %-
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 25 117 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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