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- PDB-6eja: Human Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG -

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Basic information

Entry
Database: PDB / ID: 6eja
TitleHuman Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG
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
Protein AMBP / Xylosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 1.3Nov 13, 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)87,3423
Polymers87,3192
Non-polymers231
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Activity assay shows that this peptide is a substrate for the enzyme
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-13 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.560, 85.960, 151.220
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: 1197.125 Da / Num. of mol.: 1 / Fragment: UNP residues 210-221 / Mutation: G214Y, L220G, V221G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02760
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.94→43.48 Å / Num. obs: 64274 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 39.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.041 / Rrim(I) all: 0.087 / Net I/σ(I): 8.7 / Num. measured all: 267755 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.94-1.994.11.21947030.5770.6611.39399.5
8.68-43.483.70.0397620.9970.0210.04593.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAM

2gam


Resolution: 1.94→40.184 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.04
RfactorNum. reflection% reflection
Rfree0.2125 3183 4.96 %
Rwork0.1844 --
obs0.1858 64173 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.32 Å2 / Biso mean: 56.5414 Å2 / Biso min: 27.46 Å2
Refinement stepCycle: final / Resolution: 1.94→40.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5550 0 1 225 5776
Biso mean--42.86 45.25 -
Num. residues----703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045718
X-RAY DIFFRACTIONf_angle_d0.6317793
X-RAY DIFFRACTIONf_chiral_restr0.043835
X-RAY DIFFRACTIONf_plane_restr0.0041008
X-RAY DIFFRACTIONf_dihedral_angle_d11.2923372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.9690.34081410.3332603274499
1.969-1.99970.34111300.309426562786100
1.9997-2.03250.34721240.28462630275499
2.0325-2.06760.31241370.26732636277399
2.0676-2.10520.27961260.26162640276699
2.1052-2.14570.22991480.24222664281299
2.1457-2.18940.26541420.22392595273799
2.1894-2.23710.24521300.22142642277299
2.2371-2.28910.22661350.20912620275598
2.2891-2.34630.25881320.20332605273799
2.3463-2.40980.26151390.21282665280499
2.4098-2.48070.23841530.20672625277899
2.4807-2.56070.25511440.197926572801100
2.5607-2.65220.23421460.195726612807100
2.6522-2.75840.23251290.19626832812100
2.7584-2.88390.2051600.192639279999
2.8839-3.03590.21031440.19082628277299
3.0359-3.2260.24171170.19872691280899
3.226-3.4750.20621330.17812692282599
3.475-3.82440.19721400.1612666280699
3.8244-4.37720.1651420.14322659280197
4.3772-5.51260.17271450.1432679282497
5.5126-40.19250.20141460.18832754290095
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)
12.11640.0178-0.19282.3377-0.08870.903-0.06550.031-0.34080.0440.05660.26740.0639-0.14150.01740.37290.0356-0.01360.3817-0.01680.3444-2.687118.80754.3647
21.4730.25940.05182.47490.08450.6915-0.0266-0.257-0.23690.198-0.0183-0.01580.0387-0.04960.05430.35920.03720.00310.39380.02450.39225.491721.235956.763
31.0820.2664-0.14171.47710.06721.3672-0.006-0.16620.11080.2027-0.04770.2432-0.2855-0.22260.04180.42580.024-0.03450.3791-0.07070.3778-1.97356.252562.3909
44.7401-5.4933-0.99716.71750.56776.4821-0.4133-0.6715-1.60260.54820.03290.26390.51390.36140.3920.8509-0.13910.12310.68570.06630.6222-3.926120.598669.2099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 349 )A253 - 349
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 606 )A350 - 606
3X-RAY DIFFRACTION3chain 'A' and (resid 607 through 959 )A607 - 959
4X-RAY DIFFRACTION4chain 'B' and (resid 213 through 219 )B213 - 219

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