7BBN

Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 317)

PDB DOI: https://doi.org/10.2210/pdb7BBN/pdb

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

Deposited: 2020-12-18 Released: 2022-01-19
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: 1.68 Å
R-Value Free: 0.220
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 317)

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

To be published.

Macromolecule Content

Total Structure Weight: 87.18 kDa
Atom Count: 6,015
Modelled Residue Count: 727
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation Factor Tu	A, B	393	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.220
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.342	α = 90
b = 100.289	β = 90
c = 160.719	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Majumdar, S.

Bergfors, T.

Sanyal, S.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-05946
Swedish Research Council	Sweden	2018-05498
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: 2022-01-19
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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7BBN

Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 317)

Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 317)

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)