[English] 日本語
Yorodumi
- PDB-6ejd: Human Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG -

+
Open data


ID or keywords:

Loading...

-
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 / : / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / 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 / : / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process / IgA binding / 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 / female pregnancy / serine-type endopeptidase inhibitor activity / carbohydrate binding / : / 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: 2.684 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more