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- PDB-1dzy: L-Fuculose-1-Phosphate Aldolase from Escherichia coli Mutant E214A -

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Basic information

Entry
Database: PDB / ID: 1dzy
TitleL-Fuculose-1-Phosphate Aldolase from Escherichia coli Mutant E214A
ComponentsL-FUCULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE (ALDEHYDE) / ALDOLASE (CLASS II) / BACTERIAL L-FUCOSE METABOLISM / CLEAVAGE OF L-FUCULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE 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
BETA-MERCAPTOETHANOL / L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.44 Å
AuthorsJoerger, A.C. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Catalytic Action of Fuculose 1-Phosphate Aldolase (Class II) as Derived from Structure-Directed Mutagenesis
Authors: Joerger, A.C. / Gosse, C. / Fessner, W.-D. / Schulz, G.E.
#1: 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.
#2: 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
DepositionMar 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: diffrn_source / exptl_crystal_grow ...diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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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)24,0835
Polymers23,7471
Non-polymers3364
Water1,78399
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)96,33220
Polymers94,9894
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)93.800, 93.800, 42.900
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: 23747.283 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: E214A SUBSTITUTION PERFORMED WITH KUNKEL METHOD USING M13MP19
Plasmid: PKKFA2-E214A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 105 / References: UniProt: P0AB87, L-fuculose-phosphate aldolase
#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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN P ENGINEERED MUTATION GLU214ALA
Sequence detailsPHE: THE 9 C-TERMINAL RESIDUES (LYS 207 - GLU 215) WERE NOT SEEN IN THE DENSITY MAPS

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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: 38 %
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

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS XP-18H / Wavelength: 1.5418
DetectorType: SIEMENS X-1000 CCD / Detector: CCD / Date: Dec 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→10 Å / Num. obs: 6829 / % possible obs: 92 % / Redundancy: 4.1 % / Rsym value: 0.087 / Net I/σ(I): 8.2
Reflection shellResolution: 2.44→2.52 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.21 / % possible all: 85

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 2.44→10 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 -6 %RANDOM
Rwork0.149 ---
obs-6829 92 %-
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 2.44→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 15 99 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
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

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