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- PDB-6ejb: Human Xylosyltransferase 1 in complex with peptide QEEEGSAGGQGG -

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Basic information

Entry
Database: PDB / ID: 6ejb
TitleHuman Xylosyltransferase 1 in complex with peptide QEEEGSAGGQGG
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 / nuclear membrane / blood microparticle / 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: 2.557 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)87,3223
Polymers87,2272
Non-polymers951
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: This peptide is a substrate for this enzyme, as determined by activity assay.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.475, 86.694, 152.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 86122.047 Da / Num. of mol.: 1 / Fragment: UNP residues 232-959
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XYLT1, XT1 / Cell line (production host): HEK293FS / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase
#2: Protein/peptide Protein AMBP


Mass: 1105.029 Da / Num. of mol.: 1 / Mutation: G216A, L220G, V221G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02760
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
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: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.557→76.42 Å / Num. obs: 29622 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 36.15 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.112 / Rrim(I) all: 0.233 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.56-2.634.11.27821670.4730.7421.486100
11.45-76.4240.0814070.9920.0410.09199.9

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Processing

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

2gam


Resolution: 2.557→76.321 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.71
RfactorNum. reflection% reflection
Rfree0.2795 1451 4.93 %
Rwork0.2393 --
obs0.2412 29426 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.99 Å2 / Biso mean: 44.3944 Å2 / Biso min: 19.06 Å2
Refinement stepCycle: final / Resolution: 2.557→76.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 5 10 5623
Biso mean--76.17 29.56 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025779
X-RAY DIFFRACTIONf_angle_d0.4757873
X-RAY DIFFRACTIONf_chiral_restr0.039845
X-RAY DIFFRACTIONf_plane_restr0.0031017
X-RAY DIFFRACTIONf_dihedral_angle_d10.723411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.557-2.64840.41891240.37542610273494
2.6484-2.75440.40541540.3422750290499
2.7544-2.87980.36961450.322127792924100
2.8798-3.03160.38081380.309127792917100
3.0316-3.22160.35571530.28927762929100
3.2216-3.47030.3171370.261727912928100
3.4703-3.81950.24471590.218628112970100
3.8195-4.37220.22971440.1928222966100
4.3722-5.50820.18651360.173428703006100
5.5082-76.3550.23391610.205829873148100
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)
10.9080.3791-0.69741.23540.10020.7488-0.023-0.0114-0.26370.0802-0.01290.08730.0236-0.12170.01140.2230.0144-0.0290.26760.04690.4291-1.316818.703355.8807
20.85640.34030.11621.67430.00740.6832-0.0375-0.1491-0.12570.07950.0042-0.05870.0208-0.00910.02520.25850.03430.01190.24880.00770.37946.90922.906757.7661
30.74590.1077-0.28041.23150.01591.33620.0113-0.16040.12110.0858-0.06790.1796-0.2008-0.13830.03960.31170.0348-0.01820.2871-0.06350.3585-3.966157.721562.8873
48.05051.33875.06614.79260.80926.36170.0537-1.3075-0.12680.510.40520.04630.28360.2682-0.39960.6686-0.02960.04180.5598-0.01210.4942-3.095121.497370.6461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 348 )A252 - 348
2X-RAY DIFFRACTION2chain 'A' and (resid 349 through 628 )A349 - 628
3X-RAY DIFFRACTION3chain 'A' and (resid 629 through 959 )A629 - 959
4X-RAY DIFFRACTION4chain 'B' and (resid 211 through 220 )B211 - 220

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