6BDB | pdb_00006bdb

I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex)

PDB DOI: https://doi.org/10.2210/pdb6BDB/pdb
NAKB: 6BDB

Classification: HYDROLASE
Organism(s): Ophiostoma novo-ulmi subsp. americana, Ophiostoma novo-ulmi
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-10-22 Released: 2018-10-24
Deposition Author(s): Brown, C., Zhang, K., McMurrough, T.A., Laforet, M., Gloor, G.B., Edgell, D.R., Junop, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.206 (Depositor), 0.208 (DCC)
R-Value Work:
0.185 (Depositor), 0.192 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex)

Laforet, M., McMurrough, T.A., Brown, C., Junop, M., Zhang, K., Gloor, G.B.

To be published.

Macromolecule Content

Total Structure Weight: 51.11 kDa
Atom Count: 3,983
Modeled Residue Count: 347
Deposited Residue Count: 359
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein 3/homing endonuclease-like protein fusion	A	307	Ophiostoma novo-ulmi subsp. americana	Mutation(s): 2 Gene Names: HEG fusion, rps3
UniProt
Find proteins for Q4VWW5 (Ophiostoma novo-ulmi subsp. americana) Explore Q4VWW5 Go to UniProtKB: Q4VWW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4VWW5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (26-MER)	B	26	Ophiostoma novo-ulmi
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (26-MER)	C	26	Ophiostoma novo-ulmi
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.206 (Depositor), 0.208 (DCC)
R-Value Work: 0.185 (Depositor), 0.192 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.37	α = 90
b = 67.19	β = 90
c = 169.7	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

McMurrough, T.A.

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.