1UD9

Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii

PDB DOI: https://doi.org/10.2210/pdb1UD9/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Sulfurisphaera tokodaii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-04-28 Released: 2004-06-15
Deposition Author(s): Tanabe, E., Yasutake, Y., Tanaka, Y., Yao, M., Tsumoto, K., Kumagai, I., Tanaka, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.238
R-Value Work: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii

Tanabe, E., Yasutake, Y., Tanaka, Y., Yao, M., Tsumoto, K., Kumagai, I., Tanaka, I.

To be published.

Macromolecule Content

Total Structure Weight: 110.52 kDa
Atom Count: 7,996
Modelled Residue Count: 960
Deposited Residue Count: 980
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase sliding clamp A	A, B, C, D	245	Sulfurisphaera tokodaii	Mutation(s): 0
UniProt
Find proteins for Q975N2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q975N2 Go to UniProtKB: Q975N2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q975N2
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 AA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	AA [auth D] E [auth A] F [auth A] G [auth A] H [auth A] AA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.238
R-Value Work: 0.202
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.4	α = 90
b = 75.44	β = 98.83
c = 88.14	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-06-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-15
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations