8UBS

Crystal structure of NrdJ-1 split intein fusion

PDB DOI: https://doi.org/10.2210/pdb8UBS/pdb

Classification: SPLICING
Organism(s): marine metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-24 Released: 2024-10-09
Deposition Author(s): Kofoed, C., Ye, X., Jeffrey, P.D., Muir, T.W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Cell surface sculpting using logic-gated protein actuators

Muir, T.W., Kofoed, C., Ye, X., Jeffrey, P.

To be published.

Macromolecule Content

Total Structure Weight: 68.22 kDa
Atom Count: 5,213
Modelled Residue Count: 600
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrdJ-1	A, B, C, D	151	marine metagenome	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT (Subject of Investigation/LOI) Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	E [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth C], Q [auth C], R [auth D], S [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.180 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.793	α = 90
b = 84.383	β = 90
c = 174.709	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R01GM086868-25
European Molecular Biology Organization (EMBO)	European Union	EMBO ALTF 1189-2020