6DHW

Crystal structure of primase iron-sulfur domain (266-457)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.013 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs.

Holt, M.E.Salay, L.E.O'Brien, E.Barton, J.K.Chazin, W.J.

(2018) PLoS ONE 13: e0209345-e0209345


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase large subunit
A, B
192Homo sapiensMutation(s): 0 
Gene Names: PRIM2 (PRIM2A)
EC: 2.7.7.-
Find proteins for P49643 (Homo sapiens)
Go to Gene View: PRIM2
Go to UniProtKB:  P49643
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.013 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/589 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 110.193α = 90.00
b = 52.560β = 115.08
c = 88.774γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM118089

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-02
    Type: Data collection, Database references