[English] 日本語
Yorodumi
- PDB-6pt9: Crystal structure of PsS1_NC C84S in complex with k-neocarrabiose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pt9
TitleCrystal structure of PsS1_NC C84S in complex with k-neocarrabiose
Componentsexo-2S-iota carrageenan S1 sulfatase
KeywordsHYDROLASE / S1 sulfatase
Function / homologySulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 3,6-anhydro-D-galactose / 4-O-sulfo-beta-D-galactopyranose / Sulfatase
Function and homology information
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsHettle, A.G. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2019
Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.
Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B.
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: exo-2S-iota carrageenan S1 sulfatase
B: exo-2S-iota carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,64511
Polymers113,3572
Non-polymers1,2879
Water12,160675
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-16 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.692, 101.793, 170.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 473
2010B3 - 473

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein exo-2S-iota carrageenan S1 sulfatase


Mass: 56678.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Strain: PS47 / Gene: EU509_08820 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063KNC1*PLUS
#2: Sugar ChemComp-G4S / 4-O-sulfo-beta-D-galactopyranose / 4-O-sulfo-beta-D-galactose / 4-O-sulfo-D-galactose / 4-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O9S
IdentifierTypeProgram
DGalp[4S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
4-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-Galp4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 682 molecules

#3: Chemical ChemComp-9RN / 3,6-anhydro-D-galactose


Mass: 162.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Hepes, Na acetate trihydrate, arginine, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.66→39.33 Å / Num. obs: 119231 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.5
Reflection shellResolution: 1.66→1.75 Å / Rmerge(I) obs: 0.603 / Num. unique obs: 17125

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PT4

6pt4


Resolution: 1.66→38.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.981 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.202 6033 5.1 %RANDOM
Rwork0.175 ---
obs0.1764 113109 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.64 Å2 / Biso mean: 16.511 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.6 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.66→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7513 0 77 675 8265
Biso mean--21.89 22.09 -
Num. residues----945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176940
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.6610676
X-RAY DIFFRACTIONr_angle_other_deg1.471.5916162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0622.419430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.533151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4611548
X-RAY DIFFRACTIONr_chiral_restr0.0880.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021682
Refine LS restraints NCS

Ens-ID: 1 / Number: 16450 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 439 -
Rwork0.247 8156 -
all-8595 -
obs--98.25 %

+
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