3HM2

Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.205 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae

Kim, Y.Bigelow, L.Keigher, L.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
precorrin-6Y C5,15-methyltransferase
A, B, C, D, E, F, G, H
178Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)Mutation(s): 0 
Find proteins for Q6NHA4 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Go to UniProtKB:  Q6NHA4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
D, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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Download CCD File 
A, D, F
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.205 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.782α = 90.00
b = 113.853β = 90.12
c = 84.650γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DMphasing
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMmodel building
HKL-3000data collection
SHELXDphasing
RESOLVEmodel building
Cootmodel building
HKL-3000data reduction
SBC-Collectdata collection
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance