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- PDB-9iip: Fucokinase part of FKP with beta-L-fucose 1-phosphate -

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Basic information

Entry
Database: PDB / ID: 9iip
TitleFucokinase part of FKP with beta-L-fucose 1-phosphate
ComponentsL-fucokinase/L-fucose-1-P guanylyltransferase
KeywordsTRANSFERASE / fucose / kinase / beta-L-fucose 1-phosphate / product
Function / homology
Function and homology information


fucokinase / fucose-1-phosphate guanylyltransferase / fucokinase activity / GDP-L-fucose salvage / nucleotidyltransferase activity / ATP binding
Similarity search - Function
L-fucokinase / Fucose pyrophosphorylase domain / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / L-fucokinase/L-fucose-1-P guanylyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsKo, T.P. / Lin, S.W. / Hsu, M.F. / Lin, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural insight into the catalytic mechanism of the bifunctional enzyme l-fucokinase/GDP-fucose pyrophosphorylase.
Authors: Lin, S.W. / Ko, T.P. / Chiang, H.Y. / Wu, C.G. / Hsu, M.F. / Wang, A.H. / Lin, C.H.
History
DepositionJun 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-fucokinase/L-fucose-1-P guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1662
Polymers45,9211
Non-polymers2441
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.012, 120.770, 164.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-1151-

HOH

21A-1173-

HOH

31A-1184-

HOH

41A-1185-

HOH

51A-1187-

HOH

61A-1218-

HOH

71A-1241-

HOH

81A-1253-

HOH

91A-1258-

HOH

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Components

#1: Protein L-fucokinase/L-fucose-1-P guanylyltransferase


Mass: 45921.445 Da / Num. of mol.: 1 / Fragment: fucokinase part
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: fkp / Plasmid: pET16b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q58T34
#2: Sugar ChemComp-ED6 / 6-deoxy-1-O-phosphono-beta-L-galactopyranose


Type: L-saccharide / Mass: 244.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, Trypton, HEPES, beta-L-fucose 1-phosphate, MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 17444 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 67.25 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.9
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1726 / CC1/2: 0.737 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→25.02 Å / SU ML: 0.2786 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.4507
RfactorNum. reflection% reflection
Rfree0.2175 872 5 %
Rwork0.1859 --
obs0.1876 17428 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 95.29 Å2
Refinement stepCycle: LAST / Resolution: 2.45→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 0 187 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212853
X-RAY DIFFRACTIONf_angle_d0.53113877
X-RAY DIFFRACTIONf_chiral_restr0.0418435
X-RAY DIFFRACTIONf_plane_restr0.0042497
X-RAY DIFFRACTIONf_dihedral_angle_d13.85581687
LS refinement shellResolution: 2.45→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3586 142 -
Rwork0.3074 2706 -
obs--99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.336366166212-0.0712765270306-0.2543036020250.661035403240.6283378958110.486065432423-0.2204543845010.0142430728139-0.1596783263690.3551026265-0.0919128937187-0.148896946375-0.782068306796-0.629940006607-0.02441984295030.8298949727870.015065079379-0.07186633960950.715433420083-0.08713514602530.4366861355550.567034980261-21.0216967075-31.0391966436
20.252553814466-0.197270762648-0.2664213028780.5353667104640.3749253970670.2236358823950.144196736724-0.0585449418133-0.1862708747250.0407734327184-0.2605801380890.09825078429960.310948366939-0.6063691161764.13197206466E-50.49111523779-0.1720847199060.07732168122630.677500826319-0.03977860369610.5797668625064.03522644867-32.4321566201-21.4951443142
30.1356861971-0.06003896443650.02280472852110.3097694486950.102442183740.446621350608-0.0169604916988-0.0131808388713-0.3904406215670.139010246585-0.04800980527970.784266130992-0.218246274872-1.648934426060.06466371787420.5930373179740.2162729601450.08236758334411.83330291537-0.1385212111130.743074505589-15.5529992191-25.2245232435-29.6481167758
40.2427585017990.295913144996-0.01558466187290.3612800536720.03648152348960.0352032418362-0.470667737449-0.002965248908970.2791513233070.5147318237780.419899586714-0.443233873622-0.416300790121-0.739246353544-0.03664975882370.9748755452450.477839281282-0.06102940858251.13755209188-0.2599791551110.531373652877-13.1974780122-14.1553645522-29.1866700799
50.587789780204-0.01314632028810.5296375000610.04422410112680.04332498204750.3342365993840.21518991675-0.22166913-0.17504311318-0.0220968677463-0.475761932197-0.586434384515-0.105624816598-0.839802227468-0.0009846931278170.582859121281-0.01550407928220.009507266635670.919492697652-0.07582010023820.496382091522-1.42193723271-28.6100940173-27.9870932226
60.0559205045076-0.06748660561670.007421036444880.0759939907803-0.02035362739520.0237253027468-0.451142807853-0.3153504686580.553322244920.0506147598546-0.256626581654-0.204258694547-0.830347543735-0.2113927225950.0003659119555890.937094337317-0.0165404903186-0.003369856185781.12470023465-0.1841184987280.8565281179950.183303732356-20.662344478-20.1095240991
70.203116028134-0.2076481942420.1593028128550.332646257667-0.4232041105410.373608805077-0.0846903179505-0.3754548545370.3199577425520.00528345125595-0.06043649528890.195355539979-0.0498173980726-0.4129020882835.56145953361E-50.605976126049-0.1444192316420.07085193488770.773547639114-0.09487352541420.6442543830316.01742187664-28.7975837073-14.9919597147
81.05595868595-0.4908897776720.3474557177360.623052118663-0.2872566425840.1781315653780.177339995848-0.0719822875424-0.1964071941060.171445419894-0.0476312512647-0.2034735923950.181516881179-0.0493252883993-3.51141909504E-50.651041059176-0.2918622051840.04103981484310.538732525666-0.05136379373220.64269053298114.8561117062-40.5910568546-18.4528397248
90.0929818316835-0.06600186560560.08336139966550.09447233859910.1270276306280.3637115722660.252706684448-0.676167530798-1.104163192180.487780011772-0.337850848169-0.4967025677830.3183763687150.0107100987242-0.0001865058512440.837480125267-0.2209409935750.02407620569810.5319161238230.1078413838980.68183884087916.0256467272-46.6957720801-14.400276591
100.264948975409-0.4173754543340.4068071413990.562581306425-0.5504963628760.9272040915160.5415165318030.0340884620647-0.1566968263330.110401744315-0.2189199088720.2146363020081.835127773850.2480138349240.2233946492781.00465956552-0.3957983434130.07826805681620.440982089641-0.01348207025240.86718937485710.5423042969-53.802055499-24.3699405936
110.00735032761075-0.0979414938159-0.04565215747380.0657309336720.1475596595630.830732675859-0.1295534456670.123854103911-0.108416386049-0.7180423896380.243023845941-0.4139418724050.197258621328-0.7274988027630.0004427075051630.875299234216-0.318882087266-0.07561392914280.7079162692980.02907939004120.7153013759046.53358407674-38.9728463936-33.6955625104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 571 through 596 )
2X-RAY DIFFRACTION2chain 'A' and (resid 597 through 633 )
3X-RAY DIFFRACTION3chain 'A' and (resid 634 through 676 )
4X-RAY DIFFRACTION4chain 'A' and (resid 677 through 708 )
5X-RAY DIFFRACTION5chain 'A' and (resid 709 through 734 )
6X-RAY DIFFRACTION6chain 'A' and (resid 735 through 753 )
7X-RAY DIFFRACTION7chain 'A' and (resid 754 through 784 )
8X-RAY DIFFRACTION8chain 'A' and (resid 785 through 851 )
9X-RAY DIFFRACTION9chain 'A' and (resid 852 through 872 )
10X-RAY DIFFRACTION10chain 'A' and (resid 873 through 925 )
11X-RAY DIFFRACTION11chain 'A' and (resid 926 through 949 )

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