4DWI

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self complementary DNA, Se-dGTP and Calcium

PDB DOI: https://doi.org/10.2210/pdb4DWI/pdb
NAKB: 4DWI

Classification: TRANSFERASE/DNA
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-02-24 Released: 2013-03-27
Deposition Author(s): Gan, J.H., Abdur, R., Liu, H.H., Sheng, J., Caton-Willians, J., Soares, A.S., Huang, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.263
R-Value Work: 0.214
R-Value Observed: 0.216

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase

Gan, J.H., Abdur, R., Liu, H.H., Sheng, J., Caton-Willians, J., Soares, A.S., Huang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 73.45 kDa
Atom Count: 5,333
Modelled Residue Count: 600
Deposited Residue Count: 601
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	581	Geobacillus stearothermophilus	Mutation(s): 2 Gene Names: DPO1 EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5 Go to UniProtKB: E1C9K5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E1C9K5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APCPTPGPGPAPTPCPCPA)-3')	B, C	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9MG Query on 9MG Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	9-METHYLGUANINE C₆ H₇ N₅ O UUWJNBOCAPUTBK-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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 A] Interactions & Density 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 A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.263
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.051	α = 90
b = 93.545	β = 90
c = 105.543	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4DWI

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self complementary DNA, Se-dGTP and Calcium

Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2