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- PDB-6ej9: Human Xylosyltransferase 1 in complex with peptide QEPEGSGGGQGG -

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Basic information

Entry
Database: PDB / ID: 6ej9
TitleHuman Xylosyltransferase 1 in complex with peptide QEPEGSGGGQGG
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
PHOSPHATE ION / Protein AMBP / Xylosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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
Revision 1.3Oct 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)87,3375
Polymers87,1242
Non-polymers2133
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Activity assay demonstrates that this enzyme is active on this peptide
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-24 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.380, 86.820, 153.200
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
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: 1001.952 Da / Num. of mol.: 1 / Mutation: E212P, L220G, V221G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02760
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
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: 2.02→75.53 Å / Num. obs: 59199 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.057 / Rrim(I) all: 0.122 / Net I/σ(I): 10.9 / Num. measured all: 253525 / Scaling rejects: 0
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
2.02-2.074.41.1481918643720.7610.6131.3071.499.6
9.03-75.5340.02230337670.9990.0120.02636.698.7

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Processing

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

2gak


Resolution: 2.02→75.53 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2245 2837 4.8 %
Rwork0.2037 --
obs0.2047 59105 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.7 Å2 / Biso mean: 49.6451 Å2 / Biso min: 18.22 Å2
Refinement stepCycle: final / Resolution: 2.02→75.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 11 187 5788
Biso mean--92.07 38.53 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035781
X-RAY DIFFRACTIONf_angle_d0.5637881
X-RAY DIFFRACTIONf_chiral_restr0.042845
X-RAY DIFFRACTIONf_plane_restr0.0041014
X-RAY DIFFRACTIONf_dihedral_angle_d11.1993399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.05480.35231470.30552771291899
2.0548-2.09220.34241250.29412792291799
2.0922-2.13250.28371510.29122762291399
2.1325-2.1760.31481480.27882798294699
2.176-2.22330.30521430.26992720286398
2.2233-2.2750.28321490.26922772292199
2.275-2.33190.27611440.25992786293099
2.3319-2.3950.27561370.22812811294899
2.395-2.46550.25961520.22127952947100
2.4655-2.5450.25621390.219928312970100
2.545-2.6360.23181160.215228172933100
2.636-2.74160.27081350.21292821295699
2.7416-2.86630.23281370.21252782291999
2.8663-3.01750.23191260.20872811293798
3.0175-3.20650.27651560.213428473003100
3.2065-3.45410.20411370.20592834297199
3.4541-3.80170.21081480.18742827297599
3.8017-4.35170.19161300.16192818294897
4.3517-5.48250.15281540.14752887304199
5.4825-75.58670.18631630.19512986314998
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)
12.5367-0.6698-1.08863.7309-0.20243.8968-0.1572-0.540.04170.6938-0.0021-0.15910.3618-0.37590.13230.4829-0.0696-0.00850.38950.03730.3169-1.678421.842571.9021
21.6368-0.3248-1.04282.30450.6341.1612-0.03660.2621-0.38750.08640.01060.54760.0353-0.40520.06930.2916-0.0037-0.03050.4425-0.02470.5741-17.217313.3255.6292
32.2989-0.216-0.26432.12310.67531.0034-0.0238-0.0063-0.1451-0.06630.0112-0.2225-0.03580.08370.01370.2287-0.00830.01030.2589-0.00280.215512.739329.664750.4334
41.33490.30060.10012.19440.17410.7801-0.0083-0.1897-0.16070.2443-0.0191-0.07040.05910.02030.03560.20380.0272-0.01420.23330.02650.20336.702121.389160.5036
51.10180.2062-0.32831.30680.05121.49110.0091-0.11920.12980.1297-0.0710.1863-0.3093-0.21780.06860.27070.0432-0.04410.2497-0.05790.2348-3.8557.701563.2253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 210 through 220 )B210 - 220
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 308 )A252 - 308
3X-RAY DIFFRACTION3chain 'A' and (resid 309 through 394 )A309 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 628 )A395 - 628
5X-RAY DIFFRACTION5chain 'A' and (resid 629 through 959 )A629 - 959

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