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- PDB-3zy6: Crystal structure of POFUT1 in complex with GDP-fucose (crystal-f... -

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Basic information

Entry
Database: PDB / ID: 3zy6
TitleCrystal structure of POFUT1 in complex with GDP-fucose (crystal-form-II)
ComponentsPUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / GT-B / CATALYTIC MECHANISM / GT65
Function / homology
Function and homology information


protein O-linked fucosylation / peptide-O-fucosyltransferase / fucosyltransferase activity / peptide-O-fucosyltransferase activity / fucose metabolic process / protein O-linked glycosylation / Notch signaling pathway / endoplasmic reticulum
Similarity search - Function
GDP-fucose protein O-fucosyltransferase 1 / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsLira-Navarrete, E. / Valero-Gonzalez, J. / Villanueva, R. / Martinez-Julvez, M. / Tejero, T. / Merino, P. / Panjikar, S. / Hurtado-Guerrero, R.
CitationJournal: Plos One / Year: 2011
Title: Structural Insights Into the Mechanism of Protein O-Fucosylation.
Authors: Lira-Navarrete, E. / Valero-Gonzalez, J. / Villanueva, R. / Martinez-Julvez, M. / Tejero, T. / Merino, P. / Panjikar, S. / Hurtado-Guerrero, R.
History
DepositionAug 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5982
Polymers41,0091
Non-polymers5891
Water4,378243
1
A: PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
hetero molecules

A: PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1964
Polymers82,0172
Non-polymers1,1792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2380 Å2
ΔGint-12.2 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.583, 38.156, 68.101
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 / PEPTIDE-O-FUCOSYLTRANSFERASE 1 / O-FUCT-1 / POFUT1


Mass: 41008.746 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: Q18014, peptide-O-fucosyltransferase
#2: Chemical ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 % / Description: NONE

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Site: ESRF / Beamline: BM16 / Type: BRUKER / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.91→20 Å / Num. obs: 39386 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.37 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.27
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.97 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZY2

3zy2


Resolution: 1.91→70.48 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.339 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23733 745 2.6 %RANDOM
Rwork0.2022 ---
obs0.20314 27452 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.879 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-1.79 Å2
2--1.25 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.91→70.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 38 243 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222920
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9613965
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1323.806134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6121516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6431.51750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15222837
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89331170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9414.51128
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 60 -
Rwork0.235 1920 -
obs--96.26 %
Refinement TLS params.Method: refined / Origin x: 14.5856 Å / Origin y: -0.1174 Å / Origin z: 14.6924 Å
111213212223313233
T0.0705 Å20.0056 Å20.0035 Å2-0.0174 Å20.0077 Å2--0.0957 Å2
L0.8561 °20.023 °20.3154 °2-0.0889 °20.0229 °2--2.1687 °2
S0.0599 Å °0.0908 Å °-0.0259 Å °-0.0126 Å °0.0099 Å °0.0338 Å °0.0155 Å °-0.0851 Å °-0.0699 Å °

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