4B44 | pdb_00004b44

Bacterial translation initiation factor IF2 (1-363), complex with GDP at pH8.0

PDB DOI: https://doi.org/10.2210/pdb4B44/pdb

Classification: TRANSLATION
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-27 Released: 2013-09-18
Deposition Author(s): Simonetti, A., Urzhumtsev, A., Klaholz, B.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.271 (Depositor), 0.275 (DCC)
R-Value Work:
0.212 (Depositor), 0.256 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular Basis of GTP Hydrolysis by Bacterial Translation Initiation Factor If2

Simonetti, A., Marzi, S., Fabbretti, A., Myasnikov, A.G., Hazemann, I., Jenner, L., Urzhumtsev, A., Gualerzi, C.O., Klaholz, B.P.

To be published.

Macromolecule Content

Total Structure Weight: 40.64 kDa
Atom Count: 2,741
Modeled Residue Count: 347
Deposited Residue Count: 363
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSLATION INITIATION FACTOR IF-2	A	363	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P48515 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P48515 Go to UniProtKB: P48515
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48515
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.271 (Depositor), 0.275 (DCC)
R-Value Work: 0.212 (Depositor), 0.256 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.15	α = 90
b = 62.2	β = 90
c = 159.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2015-02-11
Changes: Structure summary
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, 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.