5VOP

Methionine synthase folate-binding domain from Thermus thermophilus HB8 native


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'.

Yamada, K.Koutmos, M.

(2018) Acta Crystallogr D Struct Biol 74: 41-51


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-methyltetrahydrofolate homocysteine S-methyltransferase
A, B
296Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
EC: 2.1.1.13
Find proteins for Q5SKM5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKM5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
C2F
Query on C2F

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Download CCD File 
A, B
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
C20 H25 N7 O6
ZNOVTXRBGFNYRX-STQMWFEESA-N
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.482α = 90.00
b = 111.482β = 90.00
c = 242.679γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States13SDG14560056

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references