6BD0 | pdb_00006bd0

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

PDB DOI: https://doi.org/10.2210/pdb6BD0/pdb
NAKB: 6BD0

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

Deposited: 2017-10-20 Released: 2018-10-24
Deposition Author(s): Brown, C., Zhang, K., Laforet, M., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.190 (Depositor), 0.191 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6BD0

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 49.99 kDa
Atom Count: 4,176
Modeled Residue Count: 350
Deposited Residue Count: 350
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein 3/homing endonuclease-like protein fusion	A	300	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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (25-MER)	B	25	Ophiostoma novo-ulmi
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (25-MER)	C	25	Ophiostoma novo-ulmi
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.190 (Depositor), 0.191 (DCC)
R-Value Work: 0.165 (Depositor), 0.166 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.88	α = 90
b = 66.74	β = 90
c = 159.83	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.