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- PDB-1e6u: GDP 4-keto-6-deoxy-D-mannose epimerase reductase -

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Basic information

Entry
Database: PDB / ID: 1e6u
TitleGDP 4-keto-6-deoxy-D-mannose epimerase reductase
ComponentsGDP-FUCOSE SYNTHETASE
KeywordsEPIMERASE/REDUCTASE / SDR / RED / EPIMERASE-REDUCTASE complex
Function / homology
Function and homology information


GDP-L-fucose synthase / GDP-L-fucose synthase activity / colanic acid biosynthetic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / ACETYLPHOSPHATE / GDP-L-fucose synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRosano, C. / Izzo, G. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Probing the Catalytic Mechanism of Gdp-4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase by Kinetic and Crystallographic Characterization of Site-Specific Mutants
Authors: Rosano, C. / Bisso, A. / Izzo, G. / Tonetti, M. / Sturla, L. / De Flora, A. / Bolognesi, M.
#1: Journal: Croatica Chemica Acta / Year: 2000
Title: The High Resolution Structure of Gdp 4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase
Authors: Rosano, C. / Izzo, G. / Sturla, L. / Bisso, A. / Tonetti, M. / Bolognesi, M.
History
DepositionAug 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GDP-FUCOSE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5768
Polymers36,1861
Non-polymers1,3907
Water6,702372
1
A: GDP-FUCOSE SYNTHETASE
hetero molecules

A: GDP-FUCOSE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,15216
Polymers72,3722
Non-polymers2,78014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3590 Å2
ΔGint-32 kcal/mol
Surface area30740 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.800, 102.800, 74.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2160-

HOH

DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GDP-FUCOSE SYNTHETASE / GDP-4-KETO 6-DEOXY-MANNOSE 3 / 5-EPIMERASE 4-REDUCTASE / MER


Mass: 36186.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UNKNOWN MOLECULE LABELED AS ACETYLPHOSPHATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P32055, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives

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Non-polymers , 5 types, 379 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-UVW / ACETYLPHOSPHATE


Mass: 140.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5O5P
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: TWO STEP NADP-DEPENDENT CONVERSION OF GDP-4-DEHYDRO-6- DEOXY-D-MANNOSE TO GDP-FUCOSE. ...FUNCTION: TWO STEP NADP-DEPENDENT CONVERSION OF GDP-4-DEHYDRO-6- DEOXY-D-MANNOSE TO GDP-FUCOSE. PATHWAY: INVOLVED IN THE BIOSYNTHESIS OF THE SLIME POLYSACCHARIDE COLANIC ACID. SECOND AND THIRD OF THE THREE STEPS IN THE BIOSYNTHESIS OF GDP-FUCOSE FROM GDP-MANNOSE. SUBUNIT: HOMODIMER. SUBCELLULAR LOCATION: CYTOPLASMIC. SIMILARITY: TO A.CAULINODANS NOLK AND TO MOUSE P35B. SIMILARITY: STRONG, TO Y.ENTEROCOLITICA WBCJ.

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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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 1.5 M LITHIUM SULPHATE, PH 6.5 0.1M TRIS BUFFER 21C
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: unknown / PH range low: 7.8 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111-20 mg/mlprotein11
21.5 Mlithium sulfate12
30.1 MMES12or Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.855
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.855 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 80994 / % possible obs: 99.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.8
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 5.5 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BWS

1bws


Resolution: 1.45→10 Å / SU B: 0.66156 / SU ML: 0.02616 / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.17 4017 5 %RANDOM
Rwork0.135 ---
obs-75989 98.9 %-
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 84 372 2947
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.04
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 Rfree: 0.167 / Rfactor Rwork: 0.127
Solvent computation
*PLUS
Displacement parameters
*PLUS

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