4GNX | pdb_00004gnx

Structure of U. maydis Replication protein A bound to ssDNA

• PDB DOI: https://doi.org/10.2210/pdb4GNX/pdb
• NAKB: 4GNX

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mycosarcoma maydis, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-08-17 Released: 2013-02-20 
• Deposition Author(s): Pavletich, N.P., Fan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.278 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Structure of

Pavletich, N.P., Fan, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 192.28 kDa 
• Atom Count: 11,350 
• Modeled Residue Count: 1,371 
• Deposited Residue Count: 1,512 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, D [auth X]	114	Mycosarcoma maydis	Mutation(s): 0  Gene Names: UM04165.1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	B, E [auth Y]	136	Mycosarcoma maydis	Mutation(s): 0  Gene Names: UM02579.1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	C, F [auth Z]	444	Mycosarcoma maydis	Mutation(s): 0  Gene Names: UM05156.1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	G [auth K], H [auth L]	62	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth C], J [auth Z]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.278 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.1	α = 90
b = 91.4	β = 97.8
c = 114.6	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Pavletich, N.P., Fan, J.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Structure summary
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary