4II9 | pdb_00004ii9

Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate

PDB DOI: https://doi.org/10.2210/pdb4II9/pdb
NAKB: 4II9

Classification: TRANSFERASE/PEPTIDE/RNA
Organism(s): Weissella viridescens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-12-20 Released: 2013-07-03
Deposition Author(s): Li de la Sierra-Gallay, I., Fonvielle, M., van Tilbeurgh, H., Arthur, M., Etheve-Quelquejeu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.209 (Depositor), 0.201 (DCC)
R-Value Work:
0.175 (Depositor), 0.167 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors

Fonvielle, M., Li de La Sierra-Gallay, I., El-Sagheer, A.H., Lecerf, M., Patin, D., Mellal, D., Mayer, C., Blanot, D., Gale, N., Brown, T., van Tilbeurgh, H., Etheve-Quelquejeu, M., Arthur, M.

(2013) Angew Chem Int Ed Engl 52: 7278-7281

PubMed: 23744707 Search on PubMed
DOI: https://doi.org/10.1002/anie.201301411
Primary Citation Related Structures:
4II9

Organizational Affiliation

Laboratoire de Recherche Moléculaire sur les Antibiotiques, Centre de Recherche des Cordeliers, Equipe 12, INSERM, U872, 75006 Paris, France.

Macromolecule Content

Total Structure Weight: 41.44 kDa
Atom Count: 3,149
Modeled Residue Count: 345
Deposited Residue Count: 351
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FemX	A	343	Weissella viridescens	Mutation(s): 0 Gene Names: femX EC: 2.3.2.10
UniProt
Find proteins for Q9EY50 (Weissella viridescens) Explore Q9EY50 Go to UniProtKB: Q9EY50
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EY50
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-mer peptide	B	5	N/A	Mutation(s): 0

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
RNA (5'-R(PCPCP*(A9Z))-3')	C	3	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
MUB Query on MUB Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	N-acetyl-alpha-muramic acid C₁₁ H₁₉ N O₈ MNLRQHMNZILYPY-MDMHTWEWSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.209 (Depositor), 0.201 (DCC)
R-Value Work: 0.175 (Depositor), 0.167 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.13	α = 90
b = 101.77	β = 102.6
c = 46.32	γ = 90

Software Package:

Software Name	Purpose
MX	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Li de la Sierra-Gallay, I.

Fonvielle, M.

van Tilbeurgh, H.

Arthur, M.

Etheve-Quelquejeu, M.

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2013-08-07
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary