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- PDB-5kxq: mouse POFUT1 in complex with GDP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5kxq
Titlemouse POFUT1 in complex with GDP
ComponentsGDP-fucose protein O-fucosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase O-fucosyltransferase GT-B inverting
Function / homology
Function and homology information


peptide-O-fucosyltransferase / fucosyltransferase activity / peptide-O-fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development / heart development ...peptide-O-fucosyltransferase / fucosyltransferase activity / peptide-O-fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development / heart development / angiogenesis / endoplasmic reticulum / membrane
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, Z. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1.
Authors: Li, Z. / Han, K. / Pak, J.E. / Satkunarajah, M. / Zhou, D. / Rini, J.M.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-fucose protein O-fucosyltransferase 1
B: GDP-fucose protein O-fucosyltransferase 1
C: GDP-fucose protein O-fucosyltransferase 1
D: GDP-fucose protein O-fucosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,35117
Polymers161,7854
Non-polymers3,56513
Water14,682815
1
A: GDP-fucose protein O-fucosyltransferase 1
B: GDP-fucose protein O-fucosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6648
Polymers80,8932
Non-polymers1,7716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-11 kcal/mol
Surface area27790 Å2
MethodPISA
2
C: GDP-fucose protein O-fucosyltransferase 1
D: GDP-fucose protein O-fucosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6879
Polymers80,8932
Non-polymers1,7947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-19 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.140, 251.820, 56.080
Angle α, β, γ (deg.)90.000, 95.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GDP-fucose protein O-fucosyltransferase 1 / Peptide-O-fucosyltransferase 1 / O-FucT-1


Mass: 40446.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pofut1 / Production host: Homo sapiens (human) / References: UniProt: Q91ZW2, peptide-O-fucosyltransferase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5M malonic acid, pH 6.0 / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 114238 / % possible obs: 94 % / Redundancy: 2.2 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.746 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIXdev_2341refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.499 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 19.45
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 5645 4.94 %0
Rwork0.1616 ---
obs0.163 114157 94.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.7 Å2 / Biso mean: 37.4461 Å2 / Biso min: 14.87 Å2
Refinement stepCycle: final / Resolution: 1.9→46.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10343 0 225 815 11383
Biso mean--40.02 44.13 -
Num. residues----1300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111013
X-RAY DIFFRACTIONf_angle_d1.12215027
X-RAY DIFFRACTIONf_chiral_restr0.0611614
X-RAY DIFFRACTIONf_plane_restr0.0081899
X-RAY DIFFRACTIONf_dihedral_angle_d17.0486517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.3241710.28573169334082
1.9216-1.94420.29291730.25873504367790
1.9442-1.96790.26331860.23313676386298
1.9679-1.99280.26011910.22063773396497
1.9928-2.0190.25311640.21653729389397
2.019-2.04670.28252030.20973697390097
2.0467-2.07590.24381980.20733798399697
2.0759-2.10690.2222190.19523597381697
2.1069-2.13990.24371800.19013800398097
2.1399-2.17490.23952190.18793670388996
2.1749-2.21240.21942150.18393647386296
2.2124-2.25270.24062000.18043782398297
2.2527-2.2960.1991800.17893607378796
2.296-2.34290.20872380.17353708394696
2.3429-2.39380.22381640.16553626379096
2.3938-2.44950.19811960.16243752394895
2.4495-2.51070.19341880.15793639382795
2.5107-2.57860.20051880.15423673386196
2.5786-2.65450.1892190.16063637385696
2.6545-2.74020.18211960.15993572376895
2.7402-2.83810.20161630.15753695385895
2.8381-2.95170.19921830.16233654383794
2.9517-3.0860.18691860.15163605379194
3.086-3.24870.18911610.16113588374993
3.2487-3.45210.19551690.15163600376993
3.4521-3.71860.15781910.13973572376393
3.7186-4.09260.15711760.13063496367291
4.0926-4.68430.14381770.12753498367590
4.6843-5.89990.14851930.14663410360390
5.8999-46.5130.18971580.17613338349685
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)
11.3675-0.4840.10420.6701-0.13330.1616-0.06810.10970.0001-0.00390.08860.14270.062-0.0428-0.00030.21010.0070.02630.22020.04030.299216.9927-54.454566.0159
21.4039-0.59120.59810.84820.08390.6822-0.0342-0.051-0.05850.19710.02550.34230.0478-0.13980.00020.2003-0.00610.07040.25160.06790.42716.4941-53.741666.1048
31.0784-0.0332-0.17490.6782-0.20221.0374-0.0642-0.09720.20120.17030.12330.04400.00640.00040.21550.01590.03030.1762-0.00150.246521.3909-50.638169.748
40.95360.2250.4930.73370.3470.8336-0.04710.31310.4756-0.1555-0.13-0.1942-0.20040.0723-0.00030.21450.01230.03720.33060.08380.381538.8472-42.053750.8799
50.5958-0.0821-0.31920.57730.32820.30920.07440.64750.0727-0.3266-0.1163-0.09660.1221-0.0004-0.00080.26750.03510.05820.47870.08970.304342.9621-51.143544.4367
61.14930.2069-0.07790.8269-0.14950.9527-0.00930.16150.1389-0.1549-0.0478-0.1406-0.03790.10630.00010.1690.01190.01450.23260.04470.227338.4587-51.272655.5825
71.732-0.76050.38850.6230.06220.3256-0.1603-0.09890.20980.16780.0965-0.3286-0.10960.1198-0.00050.22510.0169-0.06770.2415-0.02770.317526.4845-16.771474.3839
80.34640.2687-0.64320.3771-0.14722.0687-0.2912-0.1118-0.0181-0.14770.00390.3711-0.010.3429-0.44810.27420.0131-0.18660.3713-0.08670.64741.9188-21.145573.9289
90.6024-0.531-0.21250.37480.06360.5487-0.04190.07410.30770.14990.0629-0.6409-0.05060.23450.02850.2342-0.0003-0.06090.4075-0.01060.632641.7329-20.848466.3898
101.5378-0.49960.32670.88760.19390.2431-0.0544-0.0179-0.13370.14150.081-0.10260.06380.0113-0.00180.17770.0254-0.00450.1741-0.00820.219619.393-22.049169.4334
110.43010.3527-0.47140.4466-0.18560.4846-0.0840.1814-0.4553-0.3054-0.16690.29970.2889-0.08540.00060.32530.0181-0.00940.3244-0.07310.37843.3397-27.990853.8123
120.1584-0.08790.03190.4684-0.30640.23810.11570.45380.1921-0.1813-0.1795-0.005-0.12010.0033-0.00080.27520.0539-0.02910.3556-0.04180.22610.4577-13.903450.5365
130.8457-0.28940.19570.84860.111.2396-0.02160.0476-0.1156-0.0102-0.03770.020.0397-0.03960.00020.1531-0.00790.00780.1979-0.01940.20086.3868-17.874961.9524
140.5956-0.0279-0.17821.44630.65671.7838-0.0071-0.0736-0.03170.4150.0703-0.12880.03270.0020.00260.34160.0156-0.0490.1842-0.01570.1541.522810.2988.5759
150.01460.11670.13690.42010.0250.4759-0.04880.1057-0.0213-0.05620.03770.0217-0.10080.03680.00010.21390.0039-0.01350.2334-0.03680.2456-1.71515.336666.0646
161.48490.2495-0.05961.90490.42281.7140.04060.03020.1232-0.2573-0.05080.1483-0.3961-0.2343-0.00050.30590.0883-0.0160.2472-0.00920.1846-10.555217.862859.108
170.16750.32460.44420.58620.45321.3523-0.10010.1654-0.0723-0.1850.1329-0.059-0.06090.10950.00020.3853-0.03820.06580.2834-0.04510.253513.439642.21573.1625
180.23710.16650.14410.08960.01940.34530.0291-0.0220.1644-0.45540.242-0.4564-0.44320.39350.00580.383-0.1040.12690.3793-0.12150.344519.322147.861377.2022
190.8701-0.3191-0.0711.0667-0.68050.56730.2720.36540.0831-0.51210.06790.023-0.18390.32370.7920.7502-0.20110.31990.4993-0.05740.264816.008240.111858.8169
200.1644-0.16990.3370.3084-0.29420.4596-0.03480.0638-0.0655-0.72840.03670.0542-0.39-0.15560.00780.7532-0.06470.09290.4001-0.04530.26528.337641.672158.7875
210.21930.22010.38680.39250.15460.49650.06030.0744-0.22850.02220.1876-0.19350.26090.17970.01540.41340.03490.04320.3262-0.10890.31616.693430.22868.5955
220.34980.08260.35810.2194-0.03151.0305-0.037-0.1163-0.0136-0.18160.16490.0121-0.08480.39630.00040.3285-0.02420.01160.2334-0.03410.240711.207847.652289.6746
230.65240.27-0.13250.6264-0.46160.36210.06440.1516-0.1057-0.11660.05980.05150.315-0.00190.00020.35720.0021-0.04790.2448-0.05070.21-5.608639.041689.5435
240.176-0.0919-0.14040.25220.03650.15260.2189-0.3545-0.30850.2201-0.1860.28550.3879-0.4770.00270.3467-0.05910.03030.3645-0.06150.298-10.679639.94498.9854
250.75320.40530.26241.26410.32661.10050.036-0.04050.1187-0.0198-0.09730.233-0.0716-0.2053-0.00050.28480.00010.02430.2525-0.04470.2627-4.799549.85995.2949
260.3896-0.0741-0.18930.27250.3090.3374-0.0923-0.1018-0.1970.04130.0349-0.09580.2129-0.0122-0.00010.30860.0028-0.00450.2172-0.01250.22233.22339.291193.8693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 95 )A33 - 95
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 170 )A96 - 170
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 234 )A171 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 306 )A235 - 306
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 327 )A307 - 327
6X-RAY DIFFRACTION6chain 'A' and (resid 328 through 383 )A328 - 383
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 115 )B33 - 115
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 138 )B116 - 138
9X-RAY DIFFRACTION9chain 'B' and (resid 139 through 170 )B139 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 254 )B171 - 254
11X-RAY DIFFRACTION11chain 'B' and (resid 255 through 306 )B255 - 306
12X-RAY DIFFRACTION12chain 'B' and (resid 307 through 328 )B307 - 328
13X-RAY DIFFRACTION13chain 'B' and (resid 329 through 383 )B329 - 383
14X-RAY DIFFRACTION14chain 'C' and (resid 33 through 207 )C33 - 207
15X-RAY DIFFRACTION15chain 'C' and (resid 208 through 234 )C208 - 234
16X-RAY DIFFRACTION16chain 'C' and (resid 235 through 383 )C235 - 383
17X-RAY DIFFRACTION17chain 'D' and (resid 33 through 91 )D33 - 91
18X-RAY DIFFRACTION18chain 'D' and (resid 92 through 115 )D92 - 115
19X-RAY DIFFRACTION19chain 'D' and (resid 116 through 138 )D116 - 138
20X-RAY DIFFRACTION20chain 'D' and (resid 139 through 170 )D139 - 170
21X-RAY DIFFRACTION21chain 'D' and (resid 171 through 207 )D171 - 207
22X-RAY DIFFRACTION22chain 'D' and (resid 208 through 234 )D208 - 234
23X-RAY DIFFRACTION23chain 'D' and (resid 235 through 284 )D235 - 284
24X-RAY DIFFRACTION24chain 'D' and (resid 285 through 306 )D285 - 306
25X-RAY DIFFRACTION25chain 'D' and (resid 307 through 361 )D307 - 361
26X-RAY DIFFRACTION26chain 'D' and (resid 362 through 384 )D362 - 384

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