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- PDB-1fua: L-FUCULOSE 1-PHOSPHATE ALDOLASE CRYSTAL FORM T -

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Basic information

Entry
Database: PDB / ID: 1fua
TitleL-FUCULOSE 1-PHOSPHATE ALDOLASE CRYSTAL FORM T
ComponentsL-FUCULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE (ALDEHYDE) / CLASS II ALDOLASE / ZINC ENZYME
Function / homology
Function and homology information


L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / D-arabinose catabolic process / pentose catabolic process / L-fucose 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 / Resolution: 1.92 Å
AuthorsDreyer, M.K. / Schulz, G.E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Refined high-resolution structure of the metal-ion dependent L-fuculose-1-phosphate aldolase (class II) from Escherichia coli.
Authors: Dreyer, M.K. / 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.
#3: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1991
Title: Diastereoselective Enzymatic Aldol Additions: L-Rhamnulose and L-Fuculose 1-Phosphate Aldolases from E.Coli
Authors: Fessner, W.-D. / Sinerius, G. / Schneider, A. / Dreyer, M. / Schulz, G.E. / Badia, J. / Aguilar, J.
History
DepositionFeb 14, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,1415
Polymers23,8051
Non-polymers3364
Water2,144119
1
A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56420
Polymers95,2214
Non-polymers1,34316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area10610 Å2
ΔGint-195 kcal/mol
Surface area32330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.700, 93.700, 42.800
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
11A-400-

HOH

21A-479-

HOH

31A-481-

HOH

41A-486-

HOH

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Components

#1: Protein L-FUCULOSE-1-PHOSPHATE ALDOLASE


Mass: 23805.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PH 7.8 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 ECL116 / Plasmid: PKKFA2 / Gene (production host): FUCA / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P0AB87, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.97 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.6 / Method: vapor diffusion, hanging drop
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

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.62 Å / Num. obs: 19917 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 10 Å / % possible obs: 97 %
Reflection shell
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 1.96 Å / % possible obs: 93 % / Rmerge(I) obs: 0.284

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
XDSdata reduction
X-PLOR3phasing
RefinementResolution: 1.92→10 Å / σ(F): 0
Details: THE OCCUPANCY OF SULFATE ION 301 WAS REFINED TO 0.71.
RfactorNum. reflection% reflection
Rwork0.186 --
obs0.186 14541 97.1 %
Displacement parametersBiso mean: 19 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.92→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 15 119 1727
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it2.42
X-RAY DIFFRACTIONx_scbond_it2.52
X-RAY DIFFRACTIONx_scangle_it3.82.5

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