2JG3 | pdb_00002jg3

MtaqI with BAZ

PDB DOI: https://doi.org/10.2210/pdb2JG3/pdb
NAKB: 2JG3

Classification: TRANSFERASE/DNA
Organism(s): Thermus aquaticus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-02-07 Released: 2007-08-07
Deposition Author(s): Pljevaljcic, G., Scheidig, A.J., Weinhold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.226 (Depositor), 0.223 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Quantitative Labeling of Long Plasmid DNA with Nanometer Precision.

Pljevaljcic, G., Schmidt, F., Scheidig, A.J., Lurz, R., Weinhold, E.

(2007) Chembiochem 8: 1516

PubMed: 17654629 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200700294
Primary Citation Related Structures:
2JG3

Organizational Affiliation

Present address: Department of Molecular Biology, MB19, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 109.54 kDa
Atom Count: 7,895
Modeled Residue Count: 824
Deposited Residue Count: 882
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
MODIFICATION METHYLASE TAQI	A, D	421	Thermus aquaticus	Mutation(s): 0 EC: 2.1.1.72
UniProt
Find proteins for P14385 (Thermus aquaticus) Explore P14385 Go to UniProtKB: P14385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14385
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5'-D(GPTPTPCPGPAPTPGPTPCP)-3'	B, E	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
5'-D(GPAPCPAPTPCPGP6MAPAPCP)-3'	C, F	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BA2 Query on BA2 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain G [auth A] MOL2 format, chain L [auth D] MOL2 format, chain G [auth A] mmCIF format, chain L [auth D] mmCIF format, chain G [auth A]	G [auth A], L [auth D]	5'-DEOXY-5'-(ETHYLAMINO)-8-{[4-({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}AMINO)BUTYL]AMINO}ADENOSINE C₂₆ H₄₂ N₁₀ O₅ S GZOCMSGHLSHCGU-DGWADGOTSA-N		Interactions Focus chain G [auth A] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth B]	I [auth B], K [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth D] Interactions & Density Focus chain I [auth B] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226 (Depositor), 0.223 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.404	α = 90
b = 69.193	β = 92.16
c = 114.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-08-07

Deposition Author(s):

Pljevaljcic, G.

Scheidig, A.J.

Weinhold, E.

Revision History (Full details and data files)

Version 1.0: 2007-08-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Refinement description, Version format compliance
Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation, Source and taxonomy
Version 1.3: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description