3CVO

Crystal structure of a methyltransferase-like protein (spo2022) from silicibacter pomeroyi dss-3 at 1.80 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of methyltransferase-like protein of unknown function (YP_167254.1) from Silicibacter pomeroyi DSS-3 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyltransferase-like protein of unknown function
A, B, C, D
202Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)Mutation(s): 0 
Find proteins for Q5LRV1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Go to UniProtKB:  Q5LRV1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
D
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 173.391α = 90.00
b = 61.653β = 97.45
c = 96.323γ = 90.00
Software Package:
Software NamePurpose
MolProbitymodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
MAR345data collection
SOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2017-10-25
    Type: Refinement description