3M8R | pdb_00003m8r

Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-ethylated dTTP

PDB DOI: https://doi.org/10.2210/pdb3M8R/pdb
NAKB: 3M8R

Classification: Transferase/DNA
Organism(s): Thermus aquaticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-19 Released: 2010-07-07
Deposition Author(s): Diederichs, K., Marx, A., Betz, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.221 (Depositor), 0.217 (DCC)
R-Value Work:
0.180 (Depositor), 0.178 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of DNA polymerases caught processing size-augmented nucleotide probes.

Betz, K., Streckenbach, F., Schnur, A., Exner, T., Welte, W., Diederichs, K., Marx, A.

(2010) Angew Chem Int Ed Engl 49: 5181-5184

PubMed: 20572212 Search on PubMed
DOI: https://doi.org/10.1002/anie.200905724
Primary Citation Related Structures:
3M8R, 3M8S

Organizational Affiliation

Department of Chemistry, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.

Macromolecule Content

Total Structure Weight: 73.55 kDa
Atom Count: 5,224
Modeled Residue Count: 567
Deposited Residue Count: 568
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	540	Thermus aquaticus	Mutation(s): 0 Gene Names: polA, pol1 EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821 Go to UniProtKB: P19821
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19821
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCP(DOC))-3')	B	12	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(APAPAPAPGPGPCPGPCPCPGPTPGPGPTPC)-3')	C	16	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	G [auth A], J [auth A]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A]
HXZ Query on HXZ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	4'-ethylthymidine 5'-(tetrahydrogen triphosphate) C₁₂ H₂₁ N₂ O₁₄ P₃ RICQFQMPHJAPNN-YGOYTEALSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain H [auth A]	H [auth A], I [auth A], L [auth B], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.221 (Depositor), 0.217 (DCC)
R-Value Work: 0.180 (Depositor), 0.178 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.789	α = 90
b = 108.789	β = 90
c = 90.52	γ = 120

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-07-07

Deposition Author(s):

Diederichs, K.

Marx, A.

Betz, K.

Revision History (Full details and data files)

Version 1.0: 2010-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description