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- PDB-4ap5: Crystal structure of human POFUT2 -

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Basic information

Entry
Database: PDB / ID: 4ap5
TitleCrystal structure of human POFUT2
ComponentsGDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
KeywordsTRANSFERASE / GT-B / GT68
Function / homology
Function and homology information


positive regulation of protein folding / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / regulation of secretion / O-glycosylation of TSR domain-containing proteins / fucose metabolic process / regulation of epithelial to mesenchymal transition / mesoderm formation / regulation of gene expression ...positive regulation of protein folding / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / regulation of secretion / O-glycosylation of TSR domain-containing proteins / fucose metabolic process / regulation of epithelial to mesenchymal transition / mesoderm formation / regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus
Similarity search - Function
GDP-fucose protein O-fucosyltransferase 2-like / 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
GDP-fucose protein O-fucosyltransferase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.003 Å
AuthorsChen, C. / Keusch, J.J. / Klein, D. / Hess, D. / Hofsteenge, J. / Gut, H.
CitationJournal: Embo J. / Year: 2012
Title: Structure of Human Pofut2: Insights Into Thrombospondin Type 1 Repeat Fold and O-Fucosylation.
Authors: Chen, C.I. / Keusch, J.J. / Klein, D. / Hess, D. / Hofsteenge, J. / Gut, H.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
B: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7098
Polymers95,7642
Non-polymers9456
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-23.3 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.628, 118.628, 196.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6925, 0.4858, -0.5333), (0.4627, -0.268, -0.845), (-0.5535, -0.8319, -0.03923)
Vector: 110.2, -76.68, -4.601)

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Components

#1: Protein GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2 / PEPTIDE-O-FUCOSYLTRANSFERASE 2 / O-FUCT-2 / PROTEIN O-FUCOSYLTRANSFERASE 2


Mass: 47882.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y2G5, peptide-O-fucosyltransferase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 12% PEG 20000, 0.02 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 31375 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 50.89 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 21
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / % possible all: 71.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 3.003→29.657 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1593 5.1 %
Rwork0.1735 --
obs0.1767 31318 96.26 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.628 Å2 / ksol: 0.271 e/Å3
Displacement parametersBiso mean: 54.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.5583 Å20 Å20 Å2
2--3.5583 Å20 Å2
3----7.1166 Å2
Refinement stepCycle: LAST / Resolution: 3.003→29.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 58 116 6676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086764
X-RAY DIFFRACTIONf_angle_d1.2759161
X-RAY DIFFRACTIONf_dihedral_angle_d16.9762531
X-RAY DIFFRACTIONf_chiral_restr0.094947
X-RAY DIFFRACTIONf_plane_restr0.0061171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0034-3.10020.35861120.30751934X-RAY DIFFRACTION70
3.1002-3.21090.38951410.27582475X-RAY DIFFRACTION89
3.2109-3.33930.29681370.23112756X-RAY DIFFRACTION100
3.3393-3.4910.30361520.20742770X-RAY DIFFRACTION100
3.491-3.67480.27351460.19872770X-RAY DIFFRACTION100
3.6748-3.90450.25531310.18352784X-RAY DIFFRACTION100
3.9045-4.20520.22451410.15082808X-RAY DIFFRACTION100
4.2052-4.6270.19271700.11952778X-RAY DIFFRACTION100
4.627-5.29320.16841560.12072831X-RAY DIFFRACTION100
5.2932-6.65640.21331550.15572848X-RAY DIFFRACTION100
6.6564-29.65840.18981520.16872971X-RAY DIFFRACTION100
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)
11.0867-0.0808-0.34541.97490.45151.7404-0.04610.1489-0.0111-0.23020.03290.0254-0.0629-0.0070.01810.0744-0.0607-0.05220.09550.03560.04643.9852-25.1442-12.9533
21.56660.57970.17342.36020.66761.8241-0.0914-0.00920.11790.07110.0428-0.1597-0.23430.08620.03170.2423-0.0711-0.02070.0843-0.02260.090353.8713-7.90378.0239
31.14250.17740.50640.87690.62841.56920.0111-0.13440.07410.15690.2167-0.23830.22710.5761-0.04550.21220.1275-0.07940.5246-0.15640.163974.3836-38.9335-7.8663
40.9148-0.0950.73170.89260.37452.35240.0458-0.0553-0.20380.24080.1623-0.16510.73670.4444-0.120.40130.1071-0.04420.2939-0.07180.096663.7987-56.3249-28.6723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 41:243)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 244:429)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 41:243)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 244:429)

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