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.

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 4GNX

This is version 1.2 of the entry. See complete history.

Literature

Structure of

Pavletich, N.P., Fan, J.

To be published.

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar nucleic acids by:

(by identity cutoff)

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth Z] SDF format, chain I [auth C] MOL2 format, chain J [auth Z] MOL2 format, chain I [auth C] mmCIF format, chain J [auth Z] mmCIF format, chain I [auth C]	I [auth C], J [auth Z]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth Z] Interactions & Density Focus chain I [auth C] Focus chain J [auth Z]

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Pavletich, N.P.

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.