4MHQ | pdb_00004mhq

Crystal structure of human primase catalytic subunit

• PDB DOI: https://doi.org/10.2210/pdb4MHQ/pdb

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-30 Released: 2014-09-03 
• Deposition Author(s): Park, K.R., An, J.Y., Lee, Y., Youn, H.S., Lee, J.G., Kang, J.Y., Kim, T.G., Lim, J.J., Eom, S.H., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.233 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of human primase catalytic subunit

Park, K.R., An, J.Y., Lee, Y., Youn, H.S., Lee, J.G., Kang, J.Y., Kim, T.G., Lim, J.J., Eom, S.H., Wang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.64 kDa 
• Atom Count: 3,599 
• Modeled Residue Count: 400 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase small subunit	A	425	Homo sapiens	Mutation(s): 0  Gene Names: PRIM1 EC: 2.7.7 (PDB Primary Data), 2.7.7.102 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49642 (Homo sapiens) Explore P49642  Go to UniProtKB:  P49642
PHAROS:  P49642 GTEx:  ENSG00000198056

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.233 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.762	α = 90
b = 84.762	β = 90
c = 147.622	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Park, K.R., An, J.Y., Lee, Y., Youn, H.S., Lee, J.G., Kang, J.Y., Kim, T.G., Lim, J.J., Eom, S.H., Wang, J.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations