4BA9 | pdb_00004ba9

The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1

PDB DOI: https://doi.org/10.2210/pdb4BA9/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-12 Released: 2013-09-25
Deposition Author(s): Grummitt, C.G., Kilkenny, M.L., Frey, A., Roe, S.M., Oliver, A.W., Sale, J.E., Pearl, L.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.250 (Depositor), 0.262 (DCC)
R-Value Work:
0.214 (Depositor), 0.226 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Structural Basis for the Coordination of Y- Family Translesion DNA Polymerases by Rev1

Grummitt, C.G., Kilkenny, M.L., Frey, A., Roe, S.M., Oliver, A.W., Sale, J.E., Pearl, L.H.

To be published.

Macromolecule Content

Total Structure Weight: 79.03 kDa
Atom Count: 5,313
Modeled Residue Count: 627
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1	A, B, C, D, E A, B, C, D, E, F	114	Homo sapiens	Mutation(s): 0 EC: 2.7.7 (PDB Primary Data), 2.7.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT6 (Homo sapiens) Explore Q9UBT6 Go to UniProtKB: Q9UBT6
PHAROS: Q9UBT6 GTEx: ENSG00000122008
Find proteins for Q9UBZ9 (Homo sapiens) Explore Q9UBZ9 Go to UniProtKB: Q9UBZ9
PHAROS: Q9UBZ9 GTEx: ENSG00000135945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9UBT6 Q9UBZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F]	H [auth A] I [auth A] L [auth B] M [auth B] P [auth D] H [auth A], I [auth A], L [auth B], M [auth B], P [auth D], Q [auth D], T [auth E], U [auth E], W [auth F], X [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] J [auth B] K [auth B] N [auth C] O [auth D] G [auth A], J [auth B], K [auth B], N [auth C], O [auth D], R [auth E], S [auth E], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.250 (Depositor), 0.262 (DCC)
R-Value Work: 0.214 (Depositor), 0.226 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.75	α = 90
b = 105.75	β = 90
c = 424.27	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-25
Type: Initial release
Version 1.1: 2017-03-15
Changes: Source and taxonomy
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other