4G3I | pdb_00004g3i

Crystal structure of Dpo4 in complex with DNA duplex

PDB DOI: https://doi.org/10.2210/pdb4G3I/pdb
NAKB: 4G3I

Classification: TRANSFERASE/DNA
Organism(s): synthetic construct, Saccharolobus solfataricus P2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-14 Released: 2013-08-07
Deposition Author(s): Yan, Y.Y., Gan, J.H., Huang, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.294 (Depositor), 0.273 (DCC)
R-Value Work:
0.241 (Depositor), 0.249 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Dpo4 in complex with DNA duplex

Yan, Y.Y., Gan, J.H., Huang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 95.91 kDa
Atom Count: 6,238
Modeled Residue Count: 719
Deposited Residue Count: 742
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	E [auth A], F [auth B]	342	Saccharolobus solfataricus P2	Mutation(s): 0 Gene Names: dbh, dpo4, SSO2448 EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02 Go to UniProtKB: Q97W02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97W02
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA	A [auth C], C [auth E]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA	B [auth D], D [auth F]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.294 (Depositor), 0.273 (DCC)
R-Value Work: 0.241 (Depositor), 0.249 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.472	α = 75.4
b = 52.634	β = 80.35
c = 99.445	γ = 70.97

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.