6I8R | pdb_00006i8r

Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 170)

PDB DOI: https://doi.org/10.2210/pdb6I8R/pdb

Classification: TRANSLATION
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-11-20 Released: 2019-11-27
Deposition Author(s): Majumdar, S., Bergfors, T., Sanyal, S.
Funding Organization(s): Swedish Research Council, Wenner-Gren Foundation, Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.242 (Depositor), 0.198 (DCC)
R-Value Work:
0.192 (Depositor), 0.204 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 170)

Majumdar, S., Bergfors, T., Sanyal, S.

To be published.

Macromolecule Content

Total Structure Weight: 44.34 kDa
Atom Count: 3,071
Modeled Residue Count: 365
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation Factor Tu	A	394	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242 (Depositor), 0.198 (DCC)
R-Value Work: 0.192 (Depositor), 0.204 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.225	α = 90
b = 73.956	β = 90
c = 115.12	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2014-4423
Swedish Research Council	Sweden	2016-06264
Wenner-Gren Foundation	Sweden	UPD 2017-0238
Knut and Alice Wallenberg Foundation	Sweden	KAW 2017.0055

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2024-01-24
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.