6U44 | pdb_00006u44

Crystal structure of Methanoperedens nitroreducens elongation factor 2 H595N bound to GMPPCP and magnesium (monoclinic crystal form)

PDB DOI: https://doi.org/10.2210/pdb6U44/pdb

Classification: TRANSLATION
Organism(s): Candidatus Methanoperedens nitratireducens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-08-22 Released: 2020-03-18
Deposition Author(s): Fenwick, M.K., Ealick, S.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of elongation factor 2 switching

Fenwick, M.K., Ealick, S.E.

(2020) Curr Res Struct Biol 2: 25-34

DOI: https://doi.org/10.1016/j.crstbi.2020.02.001

Macromolecule Content

Total Structure Weight: 168.42 kDa
Atom Count: 11,854
Modeled Residue Count: 1,430
Deposited Residue Count: 1,506
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 2	A, B	753	Candidatus Methanoperedens nitratireducens	Mutation(s): 1 Gene Names: fusA, ANME2D_00299
UniProt
Find proteins for A0A062V290 (Candidatus Methanoperedens nitroreducens) Explore A0A062V290 Go to UniProtKB: A0A062V290
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A062V290
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP Query on GCP Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth A] N [auth B] O [auth B] F [auth A], G [auth A], I [auth A], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A]	E [auth A], H [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.322	α = 90
b = 106.814	β = 105.46
c = 98.056	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Fenwick, M.K.

Ealick, S.E.

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-04-03
Changes: Refinement description