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- PDB-3zy2: Crystal structure of POFUT1 in complex with GDP (High resolution ... -

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Basic information

Entry
Database: PDB / ID: 3zy2
TitleCrystal structure of POFUT1 in complex with GDP (High resolution dataset)
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 / : / GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 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 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,5073
Polymers41,0091
Non-polymers4982
Water6,323351
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)83,0146
Polymers82,0172
Non-polymers9964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2620 Å2
ΔGint-18.4 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.018, 38.247, 68.196
Angle α, β, γ (deg.)90.00, 103.07, 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Description: 3ZY2 WAS SOLVED FROM SAD PHASING METHODOLOGY USING A HIGHLY REDUNDANT DATASET TOGETHER WITH AN ISOMORPHOUS HIGH RESOLUTION DATASET (IN THIS CASE THIS ISOMORPHOUS HIGH RESOLUTION DATASET IS 3ZY2)

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.54→19.5 Å / Num. obs: 53812 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.54→70.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.307 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23725 1010 1.9 %RANDOM
Rwork0.20507 ---
obs0.2057 52544 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.687 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-1.05 Å2
2--1.17 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.54→70.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 29 351 3114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222818
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9453820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5523.817131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88215466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4071515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212191
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_it0.6541.51710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20722774
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17231108
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3244.51046
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: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 75 -
Rwork0.27 3858 -
obs--99.12 %
Refinement TLS params.Method: refined / Origin x: 14.7158 Å / Origin y: -19.2162 Å / Origin z: 15.0536 Å
111213212223313233
T0.0561 Å20.0048 Å2-0.002 Å2-0.0081 Å20.0071 Å2--0.0628 Å2
L0.9405 °20.0792 °20.454 °2-0.1116 °20.0038 °2--1.919 °2
S0.0595 Å °0.0656 Å °-0.0245 Å °-0.0167 Å °0.0174 Å °0.0269 Å °0.0071 Å °-0.0288 Å °-0.0769 Å °

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