[English] 日本語
Yorodumi
- PDB-2c83: CRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE PM0188 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c83
TitleCRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE PM0188
ComponentsHYPOTHETICAL PROTEIN PM0188Hypothesis
KeywordsTRANSFERASE / HYPOTHETICAL PROTEIN / PM0188 / SIALYLTRANSFERASE
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-2,3/2,6-sialyltransferase/sialidase / Sialyltransferase
Similarity search - Component
Biological speciesPASTEURELLA MULTOCIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKim, D.U. / Cho, H.S.
Citation
Journal: Bmb Rep / Year: 2008
Title: Structural analysis of sialyltransferase PM0188 from Pasteurella multocida complexed with donor analogue and acceptor sugar.
Authors: Kim, D.U. / Yoo, J.H. / Lee, Y.J. / Kim, K.S. / Cho, H.S.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural Analysis of the Sialyltransferase Cstii from Campylobacter Jejuni in Complex with a Substrate Analog
Authors: Chiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of the Alpha-2,6-Sialyltransferase Pm0188 from Pasteurella Multosida.
Authors: Kim, D.U. / Yoo, J.H. / Ryu, K. / Cho, H.S.
History
DepositionDec 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN PM0188


Theoretical massNumber of molelcules
Total (without water)45,6901
Polymers45,6901
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.930, 60.984, 64.635
Angle α, β, γ (deg.)90.00, 112.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HYPOTHETICAL PROTEIN PM0188 / Hypothesis / ALPHA-2 / 6-SIALYLTRANSFERASE PM0188


Mass: 45689.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PASTEURELLA MULTOCIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CP67, UniProt: Q15KI8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.8 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9713700, 0.9790300
DetectorType: BRUCKER / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971371
20.979031
ReflectionResolution: 1.9→30 Å / Num. obs: 30006 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.1 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→15 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1191 4 %RANDOM
Rwork0.215 ---
obs0.215 24729 82.2 %-
Solvent computationBsol: 41.8875 Å2 / ksol: 0.356479 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-5.076 Å2
2---2.377 Å20 Å2
3---3.097 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 0 132 3338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018101
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_deg1.96229
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

+
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