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- PDB-6ejd: Human Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG -

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Basic information

Entry
Database: PDB / ID: 6ejd
TitleHuman Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG
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: 2.684 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)87,3483
Polymers87,2532
Non-polymers951
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Activity assay shows this peptide is a substrate for the enzyme
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.538, 87.346, 153.629
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 / Plasmid: pCEP-Pu / Cell line (production host): HEK293FS / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase
#2: Protein/peptide Protein AMBP / Bikunin


Mass: 1131.066 Da / Num. of mol.: 1 / Fragment: UNP residues 210-221 / Mutation: G218P, 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.: 6 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: 2.69→61.9 Å / Num. obs: 26012 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.81 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.121 / Rrim(I) all: 0.258 / Net I/σ(I): 4.1 / Num. measured all: 110981 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.69-2.764.11.085768618710.5150.6061.2481.3100
12.03-61.93.90.08714013560.9910.0450.0996.699.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAK

2gak


Resolution: 2.684→61.827 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 1258 4.85 %
Rwork0.2441 24691 -
obs0.2458 25949 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.04 Å2 / Biso mean: 39.9548 Å2 / Biso min: 14.13 Å2
Refinement stepCycle: final / Resolution: 2.684→61.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 5 6 5533
Biso mean--113.93 21 -
Num. residues----702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035694
X-RAY DIFFRACTIONf_angle_d0.7347761
X-RAY DIFFRACTIONf_chiral_restr0.047834
X-RAY DIFFRACTIONf_plane_restr0.0051000
X-RAY DIFFRACTIONf_dihedral_angle_d11.1973358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6838-2.79120.3911340.35312530266494
2.7912-2.91830.35011440.332827192863100
2.9183-3.07210.34511430.307327212864100
3.0721-3.26460.31681180.29627382856100
3.2646-3.51660.31051280.259427482876100
3.5166-3.87050.2651630.228627212884100
3.8705-4.43040.2431520.198827662918100
4.4304-5.58120.25271340.192228042938100
5.5812-61.84360.22621420.221129443086100
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)
11.4251-0.1294-0.17951.272-0.12560.6692-0.12470.0454-0.38590.12180.14340.4701-0.0132-0.37250.00710.2407-0.0004-0.00260.4559-0.03370.6256-16.726113.052355.9285
20.8259-0.7614-0.26831.78360.23190.42250.02010.0672-0.2975-0.1913-0.0065-0.2188-0.10280.17350.00940.2123-0.00690.00610.1046-0.00320.364114.090231.535148.8775
30.87420.28180.17171.91180.14950.9030.0061-0.1212-0.17530.1263-0.00980.01670.1008-0.10190.01790.19580.04640.0130.17340.02240.35464.571818.940959.5097
42.6035-0.15490.34671.1266-0.32841.2218-0.0803-0.1078-0.10140.17220.1056-0.1661-0.04710.132-0.04350.2171-0.0033-0.07450.1455-0.04670.293912.554844.487458.7051
50.76820.0993-0.15820.8261-0.19741.7003-0.00360.11230.19270.07130.01610.0147-0.3302-0.04410.00520.30610.0242-0.06540.1349-0.01450.3252.950463.923954.8211
63.1892-0.947-0.32012.6364-0.39951.96660.1709-0.246-0.20870.3331-0.25830.4628-0.0736-0.00130.12690.3433-0.07590.07880.2288-0.08570.3088-7.46449.690877.3373
71.8610.00080.45671.7137-0.7911.59970.1749-0.18150.14510.0333-0.21140.4298-0.3703-0.43370.09670.33920.09870.03730.3681-0.1280.4684-14.698958.649568.6393
81.6771-0.0386-0.65862.04120.0781.6456-0.04410.00830.10430.0766-0.00220.1964-0.4396-0.26530.07830.30130.0286-0.09050.2546-0.06660.316-2.599760.794560.6254
90.98350.87931.3910.78811.20961.8984-0.0837-0.66720.1090.4198-0.0436-0.0717-0.1204-0.30040.08290.63050.1505-0.21360.4502-0.14590.6376-1.371721.580170.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 308 )A253 - 308
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 383 )A318 - 383
3X-RAY DIFFRACTION3chain 'A' and (resid 384 through 598 )A384 - 598
4X-RAY DIFFRACTION4chain 'A' and (resid 599 through 645 )A599 - 645
5X-RAY DIFFRACTION5chain 'A' and (resid 646 through 736 )A646 - 736
6X-RAY DIFFRACTION6chain 'A' and (resid 737 through 808 )A737 - 808
7X-RAY DIFFRACTION7chain 'A' and (resid 809 through 856 )A809 - 856
8X-RAY DIFFRACTION8chain 'A' and (resid 857 through 959 )A857 - 959
9X-RAY DIFFRACTION9chain 'B' and (resid 211 through 219 )B211 - 219

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