1OB2 | pdb_00001ob2

E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA

PDB DOI: https://doi.org/10.2210/pdb1OB2/pdb
NAKB: 1OB2

Classification: HYDROLASE/NUCLEAR PROTEIN
Organism(s): Escherichia coli BL21, Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2003-01-24 Released: 2004-05-27
Deposition Author(s): Kristensen, O., Nissen, P., Nyborg, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.265 (Depositor), 0.250 (DCC)
R-Value Work:
0.220 (Depositor), 0.210 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Kirromycin Defines a Specific Domain Arrangement of Elongation Factor EF-TU

Nielsen, R.C., Kristensen, O., Kjeldgaard, M., Thirup, S., Nissen, P.

To be published.

Macromolecule Content

Total Structure Weight: 69.92 kDa
Atom Count: 4,810
Modeled Residue Count: 470
Deposited Residue Count: 470
Unique protein chains: 1
Unique nucleic acid 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	393	Escherichia coli BL21	Mutation(s): 0 EC: 3.6.1.48 (PDB Primary Data), 3.6.5.3 (UniProt)
UniProt
Find proteins for P0CE48 (Escherichia coli (strain K12)) Explore P0CE48 Go to UniProtKB: P0CE48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CE48
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TRANSFER-RNA, PHE	B	77	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KIR Query on KIR Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	KIRROMYCIN C₄₃ H₆₀ N₂ O₁₂ HMSYAPGFKGSXAJ-PAHGNTJYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHA Query on PHA	B	L-PEPTIDE LINKING	C₉ H₁₁ N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.265 (Depositor), 0.250 (DCC)
R-Value Work: 0.220 (Depositor), 0.210 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.41	α = 90
b = 196.41	β = 90
c = 196.41	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
Agrovata	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-05-27

Deposition Author(s):

Kristensen, O.

Nissen, P.

Nyborg, J.

Revision History (Full details and data files)

Version 1.0: 2004-05-27
Type: Initial release
Version 1.1: 2012-11-14
Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
Version 1.2: 2015-08-19
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary