4BW9 | pdb_00004bw9

PylRS Y306G, Y384F, I405R mutant in complex with AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb4BW9/pdb

Classification: LIGASE
Organism(s): Methanosarcina mazei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-07-01 Released: 2013-07-31
Deposition Author(s): Schneider, S., Vrabel, M., Gattner, M.J., Fluegel, V., Lopez-Carillo, V., Carell, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.204 (Depositor), 0.202 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Insights Into Incorporation of Norbornene Amino Acids for Click Modification of Proteins

Schneider, S., Gattner, M.J., Vrabel, M., Flugel, V., Lopez-Carrillo, V., Prill, S., Carell, T.

(2013) Chembiochem 14: 2114

PubMed: 24027216 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201300435
Primary Citation Related Structures:
4BW9, 4BWA

PubMed Abstract:
Three for two: by using a Methanosarcina mazei PylRS triple mutant (Y306G, Y384F, I405R) the incorporation of two new exo-norbornene-containing pyrrolysine analogues was achieved. X-ray crystallographic analysis led to the identification of the crucial structural elements involved in substrate recognition by the evolved synthetase.

Organizational Affiliation

Department of Chemistry, TU Munich, Lichtenbergstrasse 4, 85748 Garching (Germany). sabine.schneider@mytum.de.

Macromolecule Content

Total Structure Weight: 34.38 kDa
Atom Count: 2,221
Modeled Residue Count: 265
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRROLYSINE--TRNA LIGASE	A	291	Methanosarcina mazei	Mutation(s): 3 EC: 6.1.1.26
UniProt
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PWY1 Go to UniProtKB: Q8PWY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PWY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP 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]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
1PE Query on 1PE 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]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.204 (Depositor), 0.202 (DCC)
R-Value Work: 0.174 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.742	α = 90
b = 105.742	β = 90
c = 69.674	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-31
Type: Initial release
Version 1.1: 2013-09-25
Changes: Database references
Version 1.2: 2013-12-25
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description