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- PDB-1e4a: L-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant Del(27) -

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Basic information

Entry
Database: PDB / ID: 1e4a
TitleL-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant Del(27)
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


L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / D-arabinose catabolic process / 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
BETA-MERCAPTOETHANOL / L-fuculose phosphate aldolase / L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / 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 1.3Jun 14, 2017Group: Database references / Refinement description / Category: refine / struct_ref_seq_dif
Item: _refine.pdbx_method_to_determine_struct / _struct_ref_seq_dif.details
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,0545
Polymers23,7181
Non-polymers3364
Water1,802100
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)96,21620
Polymers94,8734
Non-polymers1,34316
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)93.250, 93.250, 43.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein L-FUCULOSE 1-PHOSPHATE ALDOLASE


Mass: 23718.238 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: ALA27 DELETION PERFORMED WITH PHOSPHOROTHIOATE METHOD USING M13MP19
Plasmid: PKKFA2-DEL(27) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 105
References: UniProt: P11550, UniProt: P0AB87*PLUS, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN P ENGINEERED MUTATION ALA27 DELETED
Sequence detailsENGINEERED DELETION OF ALA27, THE RESIDUES AFTER THE DELETION SITE ARE NUMBERED ACCORDING TO THEIR ...ENGINEERED DELETION OF ALA27, THE RESIDUES AFTER THE DELETION SITE ARE NUMBERED ACCORDING TO THEIR POSITION IN WILD-TYPE

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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: Jan 15, 1998
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: 9818 / % possible obs: 92 % / Redundancy: 4.9 % / Rsym value: 0.068 / Net I/σ(I): 9.7
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4 / Rsym value: 0.19 / % possible all: 82
Reflection
*PLUS
Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 82 % / Num. unique obs: 795 / Rmerge(I) obs: 0.19

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→10 Å / SU B: 3.5 / SU ML: 0.08 / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.22
Details: THE 9 C-TERMINAL RESIDUES (LYS207 - GLU 215) WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -6 %RANDOM
Rwork0.156 ---
obs-9818 92 %-
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 15 100 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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