4F2R | pdb_00004f2r

DNA Polymerase I Large Fragment complex 3

PDB DOI: https://doi.org/10.2210/pdb4F2R/pdb
NAKB: 4F2R

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

Deposited: 2012-05-08 Released: 2013-07-24
Deposition Author(s): Wang, W., Beese, L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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: 150.33 kDa
Atom Count: 11,584
Modeled Residue Count: 1,202
Deposited Residue Count: 1,228
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5KWC1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

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

Find similar nucleic acids by: Sequence | 3D Structure

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

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H	2		N/A	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP Query on CTP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth D]	I [auth A], J [auth D]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain I [auth A] Focus chain J [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth D]	L [auth D], M [auth D], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	G, H	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.22	α = 90
b = 108.48	β = 90
c = 150.95	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary