4F4K | pdb_00004f4k

DNA Polymerase I Large Fragment Complex 6

PDB DOI: https://doi.org/10.2210/pdb4F4K/pdb
NAKB: 4F4K

Classification: Transferase/DNA
Organism(s): Geobacillus kaustophilus HTA426, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-05-10 Released: 2013-07-24
Deposition Author(s): Wang, W., Beese, L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structures of a High-fidelity DNA Polymerase

Wang, W., Hellinga, H.W., Beese, L.S.

To be published.

Macromolecule Content

Total Structure Weight: 149.27 kDa
Atom Count: 11,697
Modeled Residue Count: 1,199
Deposited Residue Count: 1,228
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A, B [auth D]	592	Geobacillus kaustophilus HTA426	Mutation(s): 2 Gene Names: polA, GK2730 EC: 2.7.7.7
UniProt
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KWC1 Go to UniProtKB: Q5KWC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5KWC1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(CPCPTPGPAPCPTPCP*(DDG))-3')	C [auth B], E	9	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(CPAPTPTPCPGPAPGPTPCPAPGP*G)-3')	D [auth C], F	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DG3 Query on DG3 Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ HDRRAMINWIWTNU-NTSWFWBYSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain G [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain G [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain G [auth A]	G [auth A], J [auth D], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.81	α = 90
b = 109.22	β = 90
c = 150.58	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Wang, W.

Beese, L.S.

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description