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- PDB-3fua: L-FUCULOSE-1-PHOSPHATE ALDOLASE CRYSTAL FORM K -

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Basic information

Entry
Database: PDB / ID: 3fua
TitleL-FUCULOSE-1-PHOSPHATE ALDOLASE CRYSTAL FORM K
ComponentsL-FUCULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE (ALDEHYDE) / CLASS II ALDOLASE / ZINC ENZYME / LYASE
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsDreyer, M.K. / Schulz, G.E.
Citation
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.
#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 25, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,0805
Polymers23,8051
Non-polymers2754
Water1,11762
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)96,32220
Polymers95,2214
Non-polymers1,10016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation23_655-z+1,y,x1
Buried area10180 Å2
ΔGint-164 kcal/mol
Surface area31300 Å2
MethodPISA, PQS
2
A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)577,929120
Polymers571,32824
Non-polymers6,60196
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area70940 Å2
ΔGint-1102 kcal/mol
Surface area179460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.000, 183.000, 183.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-301-

CL

21A-401-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 23805.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE CHLORIDE PRESUMABLY REPRESENTS A ROTATIONALLY DISORDERED SULFATE ION
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

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Non-polymers , 5 types, 66 molecules

#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


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


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.68 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
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-NICOLET X100 / Detector: AREA DETECTOR / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.58 Å / Num. obs: 7505 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.049
Reflection
*PLUS
Highest resolution: 2.67 Å / Num. obs: 7316 / % possible obs: 95 % / Num. measured all: 48988
Reflection shell
*PLUS
% possible obs: 77 %

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
XDSdata reduction
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→10 Å / σ(F): 0
Details: LOOP 23 - 27, WHICH IS NEAR THE ACTIVE SITE AND PARTICIPATES IN THE SUBUNIT INTERFACE, IS MOBILE, HAS ONLY POOR DENSITY AND THE COORDINATES ARE NOT RELIABLE. THE NINE C-TERMINAL RESIDUES ...Details: LOOP 23 - 27, WHICH IS NEAR THE ACTIVE SITE AND PARTICIPATES IN THE SUBUNIT INTERFACE, IS MOBILE, HAS ONLY POOR DENSITY AND THE COORDINATES ARE NOT RELIABLE. THE NINE C-TERMINAL RESIDUES CANNOT BE LOCATED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflection
Rfree0.241 -10 %
Rwork0.184 --
obs0.184 7316 95 %
Displacement parametersBiso mean: 18 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 11 62 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.6
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_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2.22
X-RAY DIFFRACTIONx_scbond_it1.82
X-RAY DIFFRACTIONx_scangle_it2.92.5

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