6PLJ | pdb_00006plj

A nucleotidyl transferase from Methanothermobacter thermautotroptrophicus (Mth528)

PDB DOI: https://doi.org/10.2210/pdb6PLJ/pdb

Classification: TRANSFERASE
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-01 Released: 2020-07-08
Deposition Author(s): Carbone, V., Schofield, L., Sutherland-Smith, A., Ronimus, R.
Funding Organization(s): Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.202 (Depositor), 0.202 (DCC)
R-Value Work:
0.171 (Depositor)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

A nucleotidyl transferase from Methanothermobacter thermautotroptrophicus (Mth528)

Carbone, V., Schofield, L., Sutherland-Smith, A., Ronimus, R.

To be published.

Macromolecule Content

Total Structure Weight: 26.06 kDa
Atom Count: 1,937
Modeled Residue Count: 216
Deposited Residue Count: 241
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nucleotidyl transferase	A	241	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH_528
UniProt
Find proteins for O26628 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26628 Go to UniProtKB: O26628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26628
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.202 (Depositor), 0.202 (DCC)
R-Value Work: 0.171 (Depositor)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.656	α = 90
b = 61.418	β = 90
c = 72.227	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
Auto-Rickshaw	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Sutherland-Smith, A.

Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	AGR1301

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.