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- PDB-1fui: L-FUCOSE ISOMERASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1fui
TitleL-FUCOSE ISOMERASE FROM ESCHERICHIA COLI
ComponentsL-FUCOSE ISOMERASE
KeywordsISOMERASE / KETOL ISOMERASE / FUCOSE METABOLISM / L-FUCOSE TO L-FUCULOSE CONVERSION
Function / homology
Function and homology information


D-arabinose isomerase / arabinose isomerase activity / L-fucose isomerase / L-fucose isomerase activity / D-arabinose catabolic process / L-fucose catabolic process / manganese ion binding / identical protein binding / cytosol
Similarity search - Function
L-fucose Isomerase; Chain A, domain 3 / L-fucose/L-arabinose isomerase, C-terminal / L-fucose Isomerase; Chain A, domain 2 / L-fucose Isomerase; Chain A, domain 2 / Rossmann fold - #1070 / L-fucose isomerase / L-fucose isomerase, N-terminal-1 / L-fucose isomerase, N-terminal-2 / L-fucose isomerase, C-terminal / L-fucose isomerase, domain 1 superfamily ...L-fucose Isomerase; Chain A, domain 3 / L-fucose/L-arabinose isomerase, C-terminal / L-fucose Isomerase; Chain A, domain 2 / L-fucose Isomerase; Chain A, domain 2 / Rossmann fold - #1070 / L-fucose isomerase / L-fucose isomerase, N-terminal-1 / L-fucose isomerase, N-terminal-2 / L-fucose isomerase, C-terminal / L-fucose isomerase, domain 1 superfamily / L-fucose isomerase, domain 2 superfamily / L-fucose isomerase, domain 3 superfamily / L-fucose isomerase, C-terminal domain / L-fucose isomerase, first N-terminal domain / L-fucose isomerase, second N-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FUCITOL / : / L-fucose isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT / Resolution: 2.5 Å
AuthorsSeemann, J.E. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Structure and mechanism of L-fucose isomerase from Escherichia coli.
Authors: Seemann, J.E. / Schulz, G.E.
History
DepositionApr 14, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 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 / diffrn_source / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_asym_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_asym_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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-FUCOSE ISOMERASE
B: L-FUCOSE ISOMERASE
C: L-FUCOSE ISOMERASE
D: L-FUCOSE ISOMERASE
E: L-FUCOSE ISOMERASE
F: L-FUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,76119
Polymers390,2976
Non-polymers1,46413
Water15,709872
1
A: L-FUCOSE ISOMERASE
B: L-FUCOSE ISOMERASE
C: L-FUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,90810
Polymers195,1493
Non-polymers7597
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-86 kcal/mol
Surface area59050 Å2
MethodPISA
2
D: L-FUCOSE ISOMERASE
E: L-FUCOSE ISOMERASE
F: L-FUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,8539
Polymers195,1493
Non-polymers7046
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-78 kcal/mol
Surface area59270 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43990 Å2
ΔGint-185 kcal/mol
Surface area102020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.300, 128.300, 239.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.006518, 0.999769, 0.020462), (-0.025836, -0.020624, 0.999453), (0.999645, 0.005985, 0.025964)32.5673, -23.2138, -9.3962
2given(-0.007417, -0.02616, 0.99963), (0.999807, -0.018406, 0.006936), (0.018218, 0.999488, 0.026291)9.1487, -33.1967, 22.957
3given(0.192898, -0.204066, -0.959764), (-0.204508, -0.965015, 0.16408), (-0.95967, 0.164629, -0.227882)168.70604, 120.16502, 184.12196
4given(-0.225024, -0.96062, 0.16301), (-0.959681, 0.189588, -0.207531), (0.168454, -0.203138, -0.964551)155.72807, 154.08958, 164.48239
5given(-0.955765, 0.187855, -0.226328), (0.191814, -0.185266, -0.963786), (-0.222983, -0.964566, 0.141038)189.13589, 134.308, 150.8387
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO TRIMERS.

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Components

#1: Protein
L-FUCOSE ISOMERASE


Mass: 65049.547 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cell line: JM105 / Cellular location: CYTOPLASM / Gene: FUCI / Plasmid: PKK223-3 / Species (production host): Escherichia coli / Cell line (production host): JM105 / Cellular location (production host): CYTOPLASM / Gene (production host): FUCI / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P69922, D-arabinose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 166.172 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: 2.01 M AMMONIUM SULFATE 2% PEG 400 1 MM MNCL2 10 MM 2-MERCAPTOETHANOL 10 MM L-FUCITOL 100 MM HEPES, PH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mML-fucitol1drop
31.55 Mammonium sulfate1drop
42 %(w/v)PEG4001drop
510 mMbeta-mercaptoethanol1drop
61 mM1dropMnCl2
70.1 MHEPES1drop
82 %(w/v)PEG4001reservoir
910 mMbeta-mercaptoethanol1reservoir
101 mM1reservoirMnCl2
110.1 MHEPES1reservoir
122.01 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 118481 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.099 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.297 / % possible all: 82
Reflection
*PLUS
Num. measured all: 273560 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 82.4 % / Rmerge(I) obs: 0.297

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT
Resolution: 2.5→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE ASYMMETRIC UNIT CONTAINS TWO TRIMERS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1192 0.9 %RANDOM
Rwork0.162 ---
obs0.162 117993 87 %-
Displacement parametersBiso mean: 33 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 4.4 Å / Luzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27342 0 81 872 28295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.56
X-RAY DIFFRACTIONx_mcangle_it5.02
X-RAY DIFFRACTIONx_scbond_it5.89
X-RAY DIFFRACTIONx_scangle_it8
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.318 115 1 %
Rwork0.242 11211 -
obs--84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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