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- PDB-6ej7: Human Xylosyltransferase 1 in complex with UDP-xylose and peptide... -

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Basic information

Entry
Database: PDB / ID: 6ej7
TitleHuman Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG
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 / Golgi cis cisterna / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / IgA binding ...protein xylosyltransferase / protein xylosyltransferase activity / Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / Golgi cis cisterna / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / IgA binding / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / negative regulation of immune response / embryonic skeletal system development / heme catabolic process / negative regulation of JNK cascade / ossification involved in bone maturation / Scavenging of heme from plasma / calcium channel inhibitor activity / protein catabolic process / serine-type endopeptidase inhibitor activity / female pregnancy / : / carbohydrate binding / nuclear membrane / blood microparticle / oxidoreductase activity / cell adhesion / mitochondrial inner membrane / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / Protein AMBP / Xylosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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_conn / struct_conn_type / 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 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn_type.id
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
Revision 1.4Oct 16, 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: Xylosyltransferase 1
B: Protein AMBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,29320
Polymers87,1972
Non-polymers2,09618
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: This enzyme transfers a xylose group on to a (Bound) peptide acceptor.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-60 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.460, 86.890, 152.910
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: 86122.047 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: 1075.003 Da / Num. of mol.: 1 / Mutation: S215A, 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


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 , 6 types, 383 molecules

#4: Chemical ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.86 %
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 0.1 M of Morpheus NPS mix.

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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→86.89 Å / Num. obs: 61497 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 30.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.077 / Rrim(I) all: 0.198 / Net I/σ(I): 9 / Num. measured all: 400825 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.056.71.78544620.6490.7451.937100
8.94-86.8960.0358050.9990.0140.03899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAK

2gak


Resolution: 2→76.455 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.67
RfactorNum. reflection% reflection
Rfree0.2298 3016 4.91 %
Rwork0.1985 --
obs0.2001 61401 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.04 Å2 / Biso mean: 45.9448 Å2 / Biso min: 19.28 Å2
Refinement stepCycle: final / Resolution: 2→76.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 188 366 6262
Biso mean--76.63 39.43 -
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036016
X-RAY DIFFRACTIONf_angle_d0.5568186
X-RAY DIFFRACTIONf_chiral_restr0.042864
X-RAY DIFFRACTIONf_plane_restr0.0031044
X-RAY DIFFRACTIONf_dihedral_angle_d11.9833533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.03130.38821420.36525862728
2.0313-2.06460.35831320.327926102742
2.0646-2.10020.33291390.308726062745
2.1002-2.13840.31351210.291526302751
2.1384-2.17950.2961470.271226302777
2.1795-2.2240.28111260.263326122738
2.224-2.27240.28451470.259926222769
2.2724-2.32520.31941440.248926202764
2.3252-2.38340.27571150.23626522767
2.3834-2.44780.31611310.235826232754
2.4478-2.51990.28791260.235626522778
2.5199-2.60120.24691290.229926562785
2.6012-2.69420.29141290.2226652794
2.6942-2.8020.27671320.208326352767
2.802-2.92960.23271500.201626402790
2.9296-3.0840.23441350.191926792814
3.084-3.27730.20711310.186626382769
3.2773-3.53030.1791420.169826832825
3.5303-3.88560.19141510.154926592810
3.8856-4.44770.1751620.149826822844
4.4477-5.60340.16181550.140727172872
5.6034-76.51090.23021300.194428883018
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)
11.82560.0299-0.25481.8608-0.08010.9034-0.03010.0093-0.2012-0.02850.00910.01730.0205-0.07480.00160.22210.0256-0.01930.2051-0.03290.25762.132422.830752.7115
20.6236-0.14240.0472.0252-0.07680.4423-0.041-0.0785-0.08640.10170.0104-0.037-0.00490.00190.03020.19150.0122-0.01090.223-0.010.2815.446832.19957.6407
31.33960.0527-0.561.16330.03361.50290.0115-0.11830.02720.1908-0.07250.2312-0.2452-0.26230.03820.30140.0312-0.01310.2805-0.06610.384-6.765356.342368.6242
41.9785-1.11432.32495.58581.71425.74190.1474-1.7333-0.31230.51750.0170.07060.1266-0.4847-0.10990.5629-0.050.1370.47810.05640.3285-2.91121.965671.3948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 383 )A252 - 383
2X-RAY DIFFRACTION2chain 'A' and (resid 384 through 721 )A384 - 721
3X-RAY DIFFRACTION3chain 'A' and (resid 722 through 959 )A722 - 959
4X-RAY DIFFRACTION4chain 'B' and (resid 211 through 220 )B211 - 220

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