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- PDB-5xfc: Serial femtosecond X-ray structure of a stem domain of human O-ma... -

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Basic information

Entry
Database: PDB / ID: 5xfc
TitleSerial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)
ComponentsProtein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
KeywordsSUGAR BINDING PROTEIN / glycosyltransferase / carbohydrate-binding domain
Function / homology
Function and homology information


beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked mannosylation / reactive gliosis / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development ...beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked mannosylation / reactive gliosis / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / myelination / sensory perception of sound / manganese ion binding / gene expression / carbohydrate binding / Golgi membrane / membrane
Similarity search - Function
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / : / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / GG-type lectin domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
4-nitrophenyl beta-D-mannopyranoside / Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 1.4 Å
AuthorsKuwabara, N. / Fumiaki, Y. / Kato, R. / Manya, H.
CitationJournal: IUCrJ / Year: 2017
Title: Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
Authors: Yamashita, K. / Kuwabara, N. / Nakane, T. / Murai, T. / Mizohata, E. / Sugahara, M. / Pan, D. / Masuda, T. / Suzuki, M. / Sato, T. / Kodan, A. / Yamaguchi, T. / Nango, E. / Tanaka, T. / ...Authors: Yamashita, K. / Kuwabara, N. / Nakane, T. / Murai, T. / Mizohata, E. / Sugahara, M. / Pan, D. / Masuda, T. / Suzuki, M. / Sato, T. / Kodan, A. / Yamaguchi, T. / Nango, E. / Tanaka, T. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Manya, H. / Endo, T. / Kato, R. / Senda, T. / Kato, H. / Iwata, S. / Ago, H. / Yamamoto, M. / Yumoto, F. / Nakatsu, T.
History
DepositionApr 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1304
Polymers35,5272
Non-polymers6022
Water3,081171
1
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0652
Polymers17,7641
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0652
Polymers17,7641
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.210, 91.050, 53.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

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Components

#1: Protein Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 / POMGnT1 / UDP-GlcNAc:alpha-D-mannoside beta-1 / 2-N-acetylglucosaminyltransferase I.2 / GnT I.2


Mass: 17763.707 Da / Num. of mol.: 2 / Fragment: UNP residues 92-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Sugar ChemComp-MBE / 4-nitrophenyl beta-D-mannopyranoside / 4-Nitrophenyl-beta-D-mannopyranoside / 4-nitrophenyl beta-D-mannoside / 4-nitrophenyl D-mannoside / 4-nitrophenyl mannoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: HEPES-NaOH, PEG4000

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.954 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.4→24 Å / Num. obs: 133050 / % possible obs: 100 % / Redundancy: 74.2929 % / CC1/2: 0.9321491 / Net I/σ(I): 3.302097
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.91-23.981111.55.45147590.86761100
2.311-2.9190.35.950.9251100
2.019-2.31179.65.450.93291100
1.835-2.01973.84.430.92451100
1.703-1.83574.23.040.85811100
1.603-1.70371.12.190.74541100
1.522-1.60365.91.550.58251100
1.456-1.52257.71.010.35441100
1.4-1.45644.30.630.17271100

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
PDB_EXTRACT3.22data extraction
CrystFELdata reduction
SHELXDEphasing
CrystFELdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→23.143 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.18
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2067 4540 3.42 %
Rwork0.1704 --
obs0.1717 132914 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.29 Å2 / Biso mean: 26.0766 Å2 / Biso min: 13.59 Å2
Refinement stepCycle: final / Resolution: 1.4→23.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 42 171 2551
Biso mean--27.12 39.02 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052441
X-RAY DIFFRACTIONf_angle_d1.0263313
X-RAY DIFFRACTIONf_chiral_restr0.072379
X-RAY DIFFRACTIONf_plane_restr0.004420
X-RAY DIFFRACTIONf_dihedral_angle_d12.085891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.40491500.36574250440099
1.4159-1.43260.31391530.326742564409100
1.4326-1.450.3561500.322143314481100
1.45-1.46840.33471440.300642424386100
1.4684-1.48770.31831500.290842804430100
1.4877-1.50810.29681520.274242524404100
1.5081-1.52960.27751550.25642774432100
1.5296-1.55250.24091510.242942774428100
1.5525-1.57670.25221590.233142924451100
1.5767-1.60250.2681500.226542634413100
1.6025-1.63020.2331520.214643274479100
1.6302-1.65980.26451520.203242284380100
1.6598-1.69170.23651540.196442954449100
1.6917-1.72620.24551520.184243094461100
1.7262-1.76380.24031510.170442484399100
1.7638-1.80480.21731510.169742584409100
1.8048-1.84990.2231540.149243074461100
1.8499-1.89990.15511510.140643104461100
1.8999-1.95580.15851530.133142484401100
1.9558-2.01890.18551530.128442864439100
2.0189-2.0910.15681500.123642874437100
2.091-2.17460.14471500.126742914441100
2.1746-2.27350.1641510.128142774428100
2.2735-2.39330.17761510.139342844435100
2.3933-2.5430.20531530.155542784431100
2.543-2.73910.20441460.16142754421100
2.7391-3.01420.20521460.170143004446100
3.0142-3.44920.17981500.167442744424100
3.4492-4.34090.20131500.162542814431100
4.3409-23.14640.22641560.184142914447100

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