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- PDB-1e4b: L-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant N29Q -

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Basic information

Entry
Database: PDB / ID: 1e4b
TitleL-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant N29Q
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 / OTHER / Resolution: 1.84 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
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)24,1395
Polymers23,8031
Non-polymers3364
Water2,018112
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)96,55620
Polymers95,2134
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)93.650, 93.650, 43.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11P-2022-

HOH

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Components

#1: Protein L-FUCULOSE 1-PHOSPHATE ALDOLASE


Mass: 23803.344 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: N29Q SUBSTITUTION PERFORMED WITH PHOSPHOROTHIOATE METHOD USING M13MP19
Plasmid: PKKFA2-N29Q / 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.: 112 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN P ENGINEERED MUTATION ASN29GLN

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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 / Detector: AREA DETECTOR / Date: May 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→10 Å / Num. obs: 16459 / % possible obs: 97 % / Redundancy: 3.9 % / Rsym value: 0.054 / Net I/σ(I): 10.4
Reflection shellResolution: 1.84→1.9 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.17 / % possible all: 91
Reflection
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 91 % / Num. unique obs: 1428 / Rmerge(I) obs: 0.17

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 1.84→10 Å / SU B: 1.7 / SU ML: 0.05 / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.13
Details: THE 9 C-TERMINAL RESIDUES (LYS207 - GLU 215) WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 -6 %RANDOM
Rwork0.165 ---
obs-16459 97 %-
Displacement parametersBiso mean: 22.6 Å2
Refinement stepCycle: LAST / Resolution: 1.84→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 15 112 1721
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
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: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS

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