[English] 日本語
Yorodumi
- PDB-1vkj: Crystal structure of heparan sulfate 3-O-sulfotransferase isoform... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vkj
TitleCrystal structure of heparan sulfate 3-O-sulfotransferase isoform 1 in the presence of PAP
Componentsheparan sulfate (glucosamine) 3-O-sulfotransferase 1
KeywordsTRANSFERASE / sulfotransferase / heparan sulfate / PAP / PAPSS
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 1 / HS-GAG biosynthesis / [heparan sulfate]-glucosamine 3-sulfotransferase activity / glycosaminoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / Golgi lumen / Golgi apparatus
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Heparan sulfate glucosamine 3-O-sulfotransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThorp, S. / Lee, K.A. / Negishi, M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure and mutational analysis of heparan sulfate 3-O-sulfotransferase isoform 1
Authors: Edavettal, S.C. / Lee, K.A. / Negishi, M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJun 1, 2004ID: 1S6T
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: heparan sulfate (glucosamine) 3-O-sulfotransferase 1
B: heparan sulfate (glucosamine) 3-O-sulfotransferase 1
C: heparan sulfate (glucosamine) 3-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2668
Polymers99,7923
Non-polymers1,4745
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)300.136, 300.136, 84.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Detailsnot known

-
Components

#1: Protein heparan sulfate (glucosamine) 3-O-sulfotransferase 1


Mass: 33264.004 Da / Num. of mol.: 3 / Fragment: G48-H311 / Mutation: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: O35310, [heparan sulfate]-glucosamine 3-sulfotransferase 1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Fragment: PAP / Mutation: PAP / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 5.53 Å3/Da / Density % sol: 77.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: .1M citrate, PEG 4K, .1M NaCl, 4mM PAP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97948 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2003
RadiationMonochromator: double crystal monochromator si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 63928 / Num. obs: 60048 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.116 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.371 / % possible all: 83.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NST

1nst


Resolution: 2.5→24.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 236486.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Molecule C is very disordered and therefore coordinates are not as accurate as in molecules A and B. Molecule C should not be used for structure interpretation or modeling purposes.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3021 5 %RANDOM
Rwork0.243 ---
obs0.243 59983 90.6 %-
all-63921 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5808 Å2 / ksol: 0.308559 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.37 Å20 Å20 Å2
2--8.37 Å20 Å2
3----16.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 91 178 6265
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it18.252
X-RAY DIFFRACTIONc_scangle_it21.212.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.438 351 4.9 %
Rwork0.415 6814 -
obs--65.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PAP2_CIS.PARPAP2.TOP

+
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