[English] 日本語
Yorodumi
- PDB-6foa: Human Xylosyltransferase 1 apo structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6foa
TitleHuman Xylosyltransferase 1 apo structure
ComponentsXylosyltransferase 1
KeywordsTRANSFERASE / Proteoglycan / Glycosyltransferase / Golgi / Xylosyltransferase
Function / homology
Function and homology information


protein xylosyltransferase / protein xylosyltransferase activity / Golgi cis cisterna / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / embryonic skeletal system development ...protein xylosyltransferase / protein xylosyltransferase activity / Golgi cis cisterna / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / embryonic skeletal system development / ossification involved in bone maturation / Golgi membrane / extracellular space / metal ion binding
Similarity search - Function
Xylosyltransferase, C-terminal / Xylosyltransferase / Xylosyltransferase C terminal / Glycosyl transferase, family 14 / Core-2/I-Branching enzyme
Similarity search - Domain/homology
PHOSPHATE ION / Xylosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.869 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
DepositionFeb 6, 2018Deposition 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4614
Polymers86,1221
Non-polymers3393
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Runs as a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-14 kcal/mol
Surface area30640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.283, 86.777, 153.257
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XYLT1, XT1 / Plasmid: pCEP-Pu / Cell line (production host): HEK-293-F / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 55-65% precipitant mix 2 (PEG8000 and ethylene glycol), 100 mM Bicine/Tris buffer at pH 7.5 100 mM of a sodium nitrate/sodium phosphate/ammonium sulphate mix.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.869→86.81 Å / Num. obs: 74977 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.048 / Rrim(I) all: 0.129 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.87-1.926.11.89154660.5010.8222.065100
8.36-86.816.50.0429690.9980.0170.04599.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.29data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAK

2gak


Resolution: 1.869→76.629 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.84
RfactorNum. reflection% reflection
Rfree0.222 3726 5.01 %
Rwork0.1953 --
obs0.1966 74376 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.19 Å2 / Biso mean: 37.4618 Å2 / Biso min: 13.69 Å2
Refinement stepCycle: final / Resolution: 1.869→76.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5513 0 20 465 5998
Biso mean--80.04 36.48 -
Num. residues----699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8694-1.89310.38131370.38622403254093
1.8931-1.9180.40131200.36842536265697
1.918-1.94430.39461290.35012553268298
1.9443-1.9720.32181280.32912574270298
1.972-2.00150.34851560.32742541269799
2.0015-2.03270.35441560.30292581273799
2.0327-2.06610.32051290.29532583271299
2.0661-2.10170.29881290.28162592272199
2.1017-2.13990.28381270.245725892716100
2.1399-2.18110.22861440.242925992743100
2.1811-2.22560.2771320.23512615274799
2.2256-2.2740.30441180.224426162734100
2.274-2.32690.25991290.21932648277799
2.3269-2.38510.25551480.210125812729100
2.3851-2.44960.2631300.208726102740100
2.4496-2.52170.23171350.194626162751100
2.5217-2.60310.22081320.193226412773100
2.6031-2.69610.20841530.184526212774100
2.6961-2.80410.23641560.183126272783100
2.8041-2.93170.22361380.180826262764100
2.9317-3.08630.21441230.179926662789100
3.0863-3.27960.21131330.173326352768100
3.2796-3.53280.2091290.164426852814100
3.5328-3.88840.1611500.141526702820100
3.8884-4.4510.15541430.134726852828100
4.451-5.60750.15641550.139827182873100
5.6075-76.69290.20561670.201428393006100
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)
11.0642-0.06810.01561.5294-0.06610.8598-0.0459-0.0385-0.2216-0.04570.01090.06140.016-0.04740.00940.1540.0301-0.00380.1666-0.01670.17631.60823.088652.9392
21.07930.19660.15462.01660.0720.648-0.0398-0.1691-0.16340.1489-0.001-0.04120.0517-0.01490.02760.1990.03210.00450.22980.02090.19666.510921.697859.3834
31.00970.2178-0.30371.08910.06131.2823-0.0003-0.14770.09460.139-0.07040.1867-0.2996-0.1980.03260.26560.045-0.03410.2262-0.05580.1958-3.820257.820763.2878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 377 )A253 - 377
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 628 )A378 - 628
3X-RAY DIFFRACTION3chain 'A' and (resid 629 through 959 )A629 - 959

+
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