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- PDB-6ej8: Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG -

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Basic information

Entry
Database: PDB / ID: 6ej8
TitleHuman Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG
Components
  • Protein AMBP
  • Xylosyltransferase 1
KeywordsTRANSFERASE / Proteoglycan / Glycosyltransferase / Golgi / Xylosyltransferase
Function / homology
Function and homology information


protein xylosyltransferase / protein xylosyltransferase activity / Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / chondroitin sulfate biosynthetic process / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process ...protein xylosyltransferase / protein xylosyltransferase activity / Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / chondroitin sulfate biosynthetic process / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / IgA binding / embryonic skeletal system development / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / ossification involved in bone maturation / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity / carbohydrate binding / collagen-containing extracellular matrix / blood microparticle / nuclear membrane / mitochondrial inner membrane / oxidoreductase activity / cell adhesion / Golgi membrane / heme binding / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Xylosyltransferase, C-terminal / Xylosyltransferase / Xylosyltransferase C terminal / Protein AMBP / Glycosyl transferase, family 14 / Core-2/I-Branching enzyme / Alpha-1-microglobulin / Lipocalin family conserved site / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. ...Xylosyltransferase, C-terminal / Xylosyltransferase / Xylosyltransferase C terminal / Protein AMBP / Glycosyl transferase, family 14 / Core-2/I-Branching enzyme / Alpha-1-microglobulin / Lipocalin family conserved site / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
PHOSPHATE ION / Protein AMBP / Xylosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBriggs, D.C. / Hohenester, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
CitationJournal: Structure / Year: 2018
Title: Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1.
Authors: Briggs, D.C. / Hohenester, E.
History
DepositionSep 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Xylosyltransferase 1
B: Protein AMBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0606
Polymers87,6262
Non-polymers4344
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Activity assay reveals that this enzyme glycosylates a this peptide substrate
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-23 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.310, 86.680, 152.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein Xylosyltransferase 1 / / Peptide O-xylosyltransferase 1 / Xylosyltransferase I / XylT-I


Mass: 86534.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XYLT1, XT1 / Plasmid: pCEP-Pu / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase
#2: Protein/peptide Protein AMBP


Mass: 1091.003 Da / Num. of mol.: 1 / Mutation: L220G, V221G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02760
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 235 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.09→57.33 Å / Num. obs: 53618 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 36.13 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Net I/σ(I): 8.9 / Num. measured all: 292129 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.145.71.26639150.5870.5741.39399.9
9.35-57.334.70.036850.9990.0150.03498.3

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAK

2gak


Resolution: 2.09→57.325 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2231 2612 4.88 %
Rwork0.1946 --
obs0.196 53548 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 572.99 Å2 / Biso mean: 55.3709 Å2 / Biso min: 25.71 Å2
Refinement stepCycle: final / Resolution: 2.09→57.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5633 0 38 232 5903
Biso mean--397.81 43.35 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045830
X-RAY DIFFRACTIONf_angle_d0.5387929
X-RAY DIFFRACTIONf_chiral_restr0.042849
X-RAY DIFFRACTIONf_plane_restr0.0031020
X-RAY DIFFRACTIONf_dihedral_angle_d12.5893432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.1280.34351250.325326472772100
2.128-2.1690.30521390.296426762815100
2.169-2.21320.30951640.284926032767100
2.2132-2.26140.30371200.276326612781100
2.2614-2.3140.32561430.25226542797100
2.314-2.37180.25171260.246526312757100
2.3718-2.4360.30031430.252426662809100
2.436-2.50760.27661480.24226672815100
2.5076-2.58860.28361210.226326622783100
2.5886-2.68110.24331160.227426802796100
2.6811-2.78840.26871570.225126552812100
2.7884-2.91530.25881450.215426632808100
2.9153-3.0690.24481310.200826732804100
3.069-3.26130.24861400.203126872827100
3.2613-3.51310.21531470.190126932840100
3.5131-3.86650.17091550.16182663281899
3.8665-4.42590.1851290.14292717284699
4.4259-5.57540.15641280.13722762289099
5.5754-57.34670.19681350.18992876301199
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)
11.878-0.3349-0.21062.0167-0.03880.7937-0.05220.0255-0.31950.06150.04540.12120.0237-0.0990.00220.2680.0279-0.0130.2971-0.01780.2429-1.485519.074355.7387
21.04130.03340.09862.0950.16270.6292-0.0274-0.1182-0.17410.10640.006-0.05660.0378-0.00250.02480.25430.0234-0.01040.29060.01290.32116.90422.929457.9291
31.43610.2844-0.20441.4041-0.60822.23770.0513-0.00210.16360.0233-0.02790.0409-0.3487-0.0131-0.03010.2790.0158-0.06190.2056-0.03950.25882.427360.904954.1056
42.9339-0.5863-0.28562.7370.25222.38150.1851-0.30730.01940.1884-0.07080.21730.0142-0.129-0.00850.386-0.0130.04290.4388-0.03590.4437-6.872950.215274.7841
51.3306-0.0019-0.39751.58350.18261.29210.0515-0.10770.0490.1681-0.12920.3072-0.3724-0.29840.03820.36890.053-0.02660.3808-0.08430.4183-7.139858.126365.3349
60.3130.48990.35510.76690.55680.41280.2008-0.552-0.1040.07760.1046-0.12540.2037-0.1689-0.23080.5586-0.0411-0.00980.50520.03840.4836-2.423821.486670.6412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 349 )A252 - 349
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 628 )A350 - 628
3X-RAY DIFFRACTION3chain 'A' and (resid 629 through 736 )A629 - 736
4X-RAY DIFFRACTION4chain 'A' and (resid 737 through 790 )A737 - 790
5X-RAY DIFFRACTION5chain 'A' and (resid 791 through 959 )A791 - 959
6X-RAY DIFFRACTION6chain 'B' and (resid 211 through 219 )B211 - 219

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